[med-svn] [populations] 04/13: Import Upstream version 1.2.33
Andreas Tille
tille at debian.org
Sat Nov 18 21:01:24 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository populations.
commit 2e2a612d6221a1afa87ef8728c7b8ab22b900c45
Author: Andreas Tille <tille at debian.org>
Date: Fri Nov 17 21:46:03 2017 +0100
Import Upstream version 1.2.33
---
CMakeLists.txt | 12 +-
COPYING | 912 ++++++++++++++++++++++-----------
README | 11 +
debian.orig/changelog | 42 --
debian.orig/compat | 1 -
debian.orig/control | 16 -
debian.orig/copyright | 13 -
debian.orig/rules | 91 ----
html/index.html | 569 ++++++++++----------
html/old_formula/WARNINGS | 3 +
html/old_formula/formules.css | 30 ++
html/old_formula/formules.html | 132 +++++
html/old_formula/images.aux | 5 +
html/old_formula/images.bbl | 38 ++
html/old_formula/images.pl | 410 +++++++++++++++
html/old_formula/images.tex | 543 ++++++++++++++++++++
html/old_formula/img1.gif | Bin 0 -> 648 bytes
html/old_formula/img1.png | Bin 0 -> 225 bytes
html/old_formula/img10.gif | Bin 0 -> 292 bytes
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html/old_formula/img7.gif | Bin 0 -> 499 bytes
html/old_formula/img7.png | Bin 0 -> 278 bytes
html/old_formula/img8.gif | Bin 0 -> 554 bytes
html/old_formula/img8.png | Bin 0 -> 531 bytes
html/old_formula/img9.gif | Bin 0 -> 814 bytes
html/old_formula/img9.png | Bin 0 -> 665 bytes
html/old_formula/index.html | 132 +++++
html/old_formula/internals.pl | 26 +
html/old_formula/labels.pl | 33 ++
html/old_formula/next_motif.gif | Bin 0 -> 172 bytes
html/old_formula/next_motif_gr.gif | Bin 0 -> 172 bytes
html/old_formula/node1.html | 138 +++++
html/old_formula/node10.html | 86 ++++
html/old_formula/node11.html | 86 ++++
html/old_formula/node12.html | 142 +++++
html/old_formula/node13.html | 180 +++++++
html/old_formula/node14.html | 82 +++
html/old_formula/node15.html | 139 +++++
html/old_formula/node16.html | 106 ++++
html/old_formula/node17.html | 83 +++
html/old_formula/node18.html | 86 ++++
html/old_formula/node19.html | 106 ++++
html/old_formula/node2.html | 159 ++++++
html/old_formula/node20.html | 145 ++++++
html/old_formula/node21.html | 102 ++++
html/old_formula/node22.html | 73 +++
html/old_formula/node3.html | 131 +++++
html/old_formula/node4.html | 83 +++
html/old_formula/node5.html | 83 +++
html/old_formula/node6.html | 86 ++++
html/old_formula/node7.html | 83 +++
html/old_formula/node8.html | 86 ++++
html/old_formula/node9.html | 83 +++
html/old_formula/previous_motif.gif | Bin 0 -> 220 bytes
html/old_formula/previous_motif_gr.gif | Bin 0 -> 220 bytes
html/old_formula/up_motif.gif | Bin 0 -> 145 bytes
html/old_formula/up_motif_gr.gif | Bin 0 -> 145 bytes
html/old_formula/warnings | 9 +
populations-1.2.32.tar.gz | Bin 0 -> 578311 bytes
src/CMakeLists.txt | 78 +--
src/arbre.cpp | 68 +--
src/arbre.h | 9 +-
src/config.h | 2 +-
src/matrices.cpp | 153 +++---
src/matrices.h | 82 ++-
src/populations | Bin 610263 -> 559493 bytes
test.svg | 220 ++++++++
test.tre | 2 +
164 files changed, 5048 insertions(+), 942 deletions(-)
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 77fd74a..4c2a899 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -63,6 +63,7 @@ ENDIF( CMAKE_BUILD_TYPE MATCHES "Release" )
#CMAKE_CXX_FLAGS_RELEASE -O3 -DNDEBUG
#CMAKE_CXX_FLAGS_RELWITHDEBINFO -O2 -g
+SET (POPULATIONS_VERSION "1.2.33")
SET(CPACK_CMAKE_GENERATOR "Unix Makefiles")
SET(CPACK_GENERATOR "STGZ;TGZ;TZ")
@@ -72,23 +73,22 @@ SET(CPACK_OUTPUT_CONFIG_FILE "./CPackConfig.cmake")
SET(CPACK_PACKAGE_DESCRIPTION_FILE ${populations_SOURCE_DIR}/COPYING)
SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Populations is population genetic software")
SET(CPACK_PACKAGE_EXECUTABLES "populations")
-SET(CPACK_PACKAGE_FILE_NAME "populations-1.2.32-Linux-i686")
-SET(CPACK_PACKAGE_INSTALL_DIRECTORY "populations 1.2.32")
-SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "populations 1.2.32")
+SET(CPACK_PACKAGE_FILE_NAME "populations-${POPULATIONS_VERSION}-Linux-i686")
+SET(CPACK_PACKAGE_INSTALL_DIRECTORY "populations ${POPULATIONS_VERSION}")
+SET(CPACK_PACKAGE_INSTALL_REGISTRY_KEY "populations ${POPULATIONS_VERSION}")
SET(CPACK_PACKAGE_NAME "populations")
SET(CPACK_PACKAGE_VENDOR "CNRS")
-SET (POPULATIONS_VERSION "1.2.32")
SET(CPACK_PACKAGE_VERSION ${POPULATIONS_VERSION})
SET(CPACK_PACKAGE_VERSION_MAJOR "1")
SET(CPACK_PACKAGE_VERSION_MINOR "2")
-SET(CPACK_PACKAGE_VERSION_PATCH "32")
+SET(CPACK_PACKAGE_VERSION_PATCH "33")
SET(CPACK_RESOURCE_FILE_LICENSE ${populations_SOURCE_DIR}/COPYING)
SET(CPACK_RESOURCE_FILE_README ${populations_SOURCE_DIR}/README)
SET(CPACK_RESOURCE_FILE_WELCOME ${populations_SOURCE_DIR}/INSTALL)
SET(CPACK_RESOURCE_FILE_LICENSE ${populations_SOURCE_DIR}/ChangeLog)
SET(CPACK_SOURCE_GENERATOR "TGZ;TZ")
SET(CPACK_SOURCE_OUTPUT_CONFIG_FILE "./CPackSourceConfig.cmake")
-SET(CPACK_SOURCE_PACKAGE_FILE_NAME "populations-1.2.32")
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "populations-${POPULATIONS_VERSION}")
SET(CPACK_SOURCE_STRIP_FILES "")
SET(CPACK_STRIP_FILES "bin/populations")
SET(CPACK_SYSTEM_NAME "Linux-i686")
diff --git a/COPYING b/COPYING
index 5b6e7c6..94a9ed0 100644
--- a/COPYING
+++ b/COPYING
@@ -1,285 +1,626 @@
- GNU GENERAL PUBLIC LICENSE
- Version 2, June 1991
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
- Copyright (C) 1989, 1991 Free Software Foundation, Inc.
- 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
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-Foundation's software and to any other program whose authors commit to
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+ All rights granted under this License are granted for the term of
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+similar laws prohibiting or restricting circumvention of such
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+ 4. Conveying Verbatim Copies.
+
+ You may convey verbatim copies of the Program's source code as you
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+ You may convey a covered work in object code form under the terms
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+modified object code on the User Product (for example, the work has
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+source code form), and must require no special password or key for
+unpacking, reading or copying.
+
+ 7. Additional Terms.
+
+ "Additional permissions" are terms that supplement the terms of this
+License by making exceptions from one or more of its conditions.
+Additional permissions that are applicable to the entire Program shall
+be treated as though they were included in this License, to the extent
+that they are valid under applicable law. If additional permissions
+apply only to part of the Program, that part may be used separately
+under those permissions, but the entire Program remains governed by
+this License without regard to the additional permissions.
+
+ When you convey a copy of a covered work, you may at your option
+remove any additional permissions from that copy, or from any part of
+it. (Additional permissions may be written to require their own
+removal in certain cases when you modify the work.) You may place
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+
+ Notwithstanding any other provision of this License, for material you
+add to a covered work, you may (if authorized by the copyright holders of
+that material) supplement the terms of this License with terms:
+
+ a) Disclaiming warranty or limiting liability differently from the
+ terms of sections 15 and 16 of this License; or
+
+ b) Requiring preservation of specified reasonable legal notices or
+ author attributions in that material or in the Appropriate Legal
+ Notices displayed by works containing it; or
+
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+
+ All other non-permissive additional terms are considered "further
+restrictions" within the meaning of section 10. If the Program as you
+received it, or any part of it, contains a notice stating that it is
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+a further restriction but permits relicensing or conveying under this
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+ If you add terms to a covered work in accord with this section, you
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+
+ Additional terms, permissive or non-permissive, may be stated in the
+form of a separately written license, or stated as exceptions;
+the above requirements apply either way.
+
+ 8. Termination.
+
+ You may not propagate or modify a covered work except as expressly
+provided under this License. Any attempt otherwise to propagate or
+modify it is void, and will automatically terminate your rights under
+this License (including any patent licenses granted under the third
+paragraph of section 11).
+
+ However, if you cease all violation of this License, then your
+license from a particular copyright holder is reinstated (a)
+provisionally, unless and until the copyright holder explicitly and
+finally terminates your license, and (b) permanently, if the copyright
+holder fails to notify you of the violation by some reasonable means
+prior to 60 days after the cessation.
+
+ Moreover, your license from a particular copyright holder is
+reinstated permanently if the copyright holder notifies you of the
+violation by some reasonable means, this is the first time you have
+received notice of violation of this License (for any work) from that
+copyright holder, and you cure the violation prior to 30 days after
+your receipt of the notice.
+
+ Termination of your rights under this section does not terminate the
+licenses of parties who have received copies or rights from you under
+this License. If your rights have been terminated and not permanently
+reinstated, you do not qualify to receive new licenses for the same
+material under section 10.
+
+ 9. Acceptance Not Required for Having Copies.
+
+ You are not required to accept this License in order to receive or
+run a copy of the Program. Ancillary propagation of a covered work
+occurring solely as a consequence of using peer-to-peer transmission
+to receive a copy likewise does not require acceptance. However,
+nothing other than this License grants you permission to propagate or
+modify any covered work. These actions infringe copyright if you do
+not accept this License. Therefore, by modifying or propagating a
+covered work, you indicate your acceptance of this License to do so.
+
+ 10. Automatic Licensing of Downstream Recipients.
+
+ Each time you convey a covered work, the recipient automatically
+receives a license from the original licensors, to run, modify and
+propagate that work, subject to this License. You are not responsible
+for enforcing compliance by third parties with this License.
+
+ An "entity transaction" is a transaction transferring control of an
+organization, or substantially all assets of one, or subdividing an
+organization, or merging organizations. If propagation of a covered
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+
+ You may not impose any further restrictions on the exercise of the
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+not impose a license fee, royalty, or other charge for exercise of
+rights granted under this License, and you may not initiate litigation
+(including a cross-claim or counterclaim in a lawsuit) alleging that
+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+ 11. Patents.
+
+ A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based. The
+work thus licensed is called the contributor's "contributor version".
+
+ A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
+by this License, of making, using, or selling its contributor version,
+but do not include claims that would be infringed only as a
+consequence of further modification of the contributor version. For
+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
this License.
- 7. If, as a consequence of a court judgment or allegation of patent
-infringement or for any other reason (not limited to patent issues),
-conditions are imposed on you (whether by court order, agreement or
+ Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
+make, use, sell, offer for sale, import and otherwise run, modify and
+propagate the contents of its contributor version.
+
+ In the following three paragraphs, a "patent license" is any express
+agreement or commitment, however denominated, not to enforce a patent
+(such as an express permission to practice a patent or covenant not to
+sue for patent infringement). To "grant" such a patent license to a
+party means to make such an agreement or commitment not to enforce a
+patent against the party.
+
+ If you convey a covered work, knowingly relying on a patent license,
+and the Corresponding Source of the work is not available for anyone
+to copy, free of charge and under the terms of this License, through a
+publicly available network server or other readily accessible means,
+then you must either (1) cause the Corresponding Source to be so
+available, or (2) arrange to deprive yourself of the benefit of the
+patent license for this particular work, or (3) arrange, in a manner
+consistent with the requirements of this License, to extend the patent
+license to downstream recipients. "Knowingly relying" means you have
+actual knowledge that, but for the patent license, your conveying the
+covered work in a country, or your recipient's use of the covered work
+in a country, would infringe one or more identifiable patents in that
+country that you have reason to believe are valid.
+
+ If, pursuant to or in connection with a single transaction or
+arrangement, you convey, or propagate by procuring conveyance of, a
+covered work, and grant a patent license to some of the parties
+receiving the covered work authorizing them to use, propagate, modify
+or convey a specific copy of the covered work, then the patent license
+you grant is automatically extended to all recipients of the covered
+work and works based on it.
+
+ A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License. You may not convey a covered
+work if you are a party to an arrangement with a third party that is
+in the business of distributing software, under which you make payment
+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
-excuse you from the conditions of this License. If you cannot
-distribute so as to satisfy simultaneously your obligations under this
-License and any other pertinent obligations, then as a consequence you
-may not distribute the Program at all. For example, if a patent
-license would not permit royalty-free redistribution of the Program by
-all those who receive copies directly or indirectly through you, then
-the only way you could satisfy both it and this License would be to
-refrain entirely from distribution of the Program.
-
-If any portion of this section is held invalid or unenforceable under
-any particular circumstance, the balance of the section is intended to
-apply and the section as a whole is intended to apply in other
-circumstances.
-
-It is not the purpose of this section to induce you to infringe any
-patents or other property right claims or to contest validity of any
-such claims; this section has the sole purpose of protecting the
-integrity of the free software distribution system, which is
-implemented by public license practices. Many people have made
-generous contributions to the wide range of software distributed
-through that system in reliance on consistent application of that
-system; it is up to the author/donor to decide if he or she is willing
-to distribute software through any other system and a licensee cannot
-impose that choice.
-
-This section is intended to make thoroughly clear what is believed to
-be a consequence of the rest of this License.
-
- 8. If the distribution and/or use of the Program is restricted in
-certain countries either by patents or by copyrighted interfaces, the
-original copyright holder who places the Program under this License
-may add an explicit geographical distribution limitation excluding
-those countries, so that distribution is permitted only in or among
-countries not thus excluded. In such case, this License incorporates
-the limitation as if written in the body of this License.
-
- 9. The Free Software Foundation may publish revised and/or new versions
-of the General Public License from time to time. Such new versions will
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Use with the GNU Affero General Public License.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
-Each version is given a distinguishing version number. If the Program
-specifies a version number of this License which applies to it and "any
-later version", you have the option of following the terms and conditions
-either of that version or of any later version published by the Free
-Software Foundation. If the Program does not specify a version number of
-this License, you may choose any version ever published by the Free Software
-Foundation.
-
- 10. If you wish to incorporate parts of the Program into other free
-programs whose distribution conditions are different, write to the author
-to ask for permission. For software which is copyrighted by the Free
-Software Foundation, write to the Free Software Foundation; we sometimes
-make exceptions for this. Our decision will be guided by the two goals
-of preserving the free status of all derivatives of our free software and
-of promoting the sharing and reuse of software generally.
-
- NO WARRANTY
-
- 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
-FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
-OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
-PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
-OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
-TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
-PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
-REPAIR OR CORRECTION.
-
- 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
-WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
-REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
-INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
-OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
-TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
-YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
-PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGES.
-
- END OF TERMS AND CONDITIONS
-
- How to Apply These Terms to Your New Programs
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
@@ -287,15 +628,15 @@ free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
-convey the exclusion of warranty; and each file should have at least
+state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
- This program is free software; you can redistribute it and/or modify
+ This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
+ the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
@@ -304,37 +645,30 @@ the "copyright" line and a pointer to where the full notice is found.
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
- along with this program; if not, write to the Free Software
- Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
-If the program is interactive, make it output a short notice like this
-when it starts in an interactive mode:
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
- Gnomovision version 69, Copyright (C) year name of author
- Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License. Of course, the commands you use may
-be called something other than `show w' and `show c'; they could even be
-mouse-clicks or menu items--whatever suits your program.
-
-You should also get your employer (if you work as a programmer) or your
-school, if any, to sign a "copyright disclaimer" for the program, if
-necessary. Here is a sample; alter the names:
-
- Yoyodyne, Inc., hereby disclaims all copyright interest in the program
- `Gnomovision' (which makes passes at compilers) written by James Hacker.
-
- <signature of Ty Coon>, 1 April 1989
- Ty Coon, President of Vice
-
-This General Public License does not permit incorporating your program into
-proprietary programs. If your program is a subroutine library, you may
-consider it more useful to permit linking proprietary applications with the
-library. If this is what you want to do, use the GNU Library General
-Public License instead of this License.
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
diff --git a/README b/README
index e69de29..6f4702b 100644
--- a/README
+++ b/README
@@ -0,0 +1,11 @@
+# Description : "populations" is a population genetics software
+#
+#
+# Copyright : Olivier Langella
+#
+# License : GPLv3
+#
+# This program is free software; you can redistribute it and/or modify *
+# it under the terms of the GNU General Public License as published by *
+# the Free Software Foundation; either version 3 of the License, or *
+# (at your option) any later version.
diff --git a/debian.orig/changelog b/debian.orig/changelog
deleted file mode 100644
index 4d95be8..0000000
--- a/debian.orig/changelog
+++ /dev/null
@@ -1,42 +0,0 @@
-populations (1.2.32-2~maverick1) maverick; urgency=low
-
- * maverick package
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 19 Feb 2010 10:18:51 +0200
-
-populations (1.2.32-2~lucid1) lucid; urgency=low
-
- * lucid package
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 19 Feb 2010 10:18:51 +0200
-
-populations (1.2.32-2~karmic1) karmic; urgency=low
-
- * qt 4.6 introduced for xmlstreamwriter
- * fixed problems reading symetric matrix (Alan Meerow warning)
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Fri, 19 Feb 2010 10:18:51 +0200
-
-populations (1.2.31-1~karmic1) karmic; urgency=low
-
- * repackaging for Ubuntu Karmic Koala
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Sun, 18 Sep 2009 10:18:51 +0200
-
-populations (1.2.31-1) unstable; urgency=low
-
- * version number updated.
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 03 Feb 2009 11:18:51 +0200
-
-populations (1.2.30-1~hardy1) hardy; urgency=low
-
- * hardy version
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 26 Nov 2008 11:18:51 +0200
-
-populations (1.2.30-1) unstable; urgency=low
-
- * Initial release.
-
- -- Olivier Langella <Olivier.Langella at moulon.inra.fr> Wed, 24 Oct 2001 11:18:51 +0200
diff --git a/debian.orig/compat b/debian.orig/compat
deleted file mode 100644
index b8626c4..0000000
--- a/debian.orig/compat
+++ /dev/null
@@ -1 +0,0 @@
-4
diff --git a/debian.orig/control b/debian.orig/control
deleted file mode 100644
index f4f2408..0000000
--- a/debian.orig/control
+++ /dev/null
@@ -1,16 +0,0 @@
-Source: populations
-Section: science
-Priority: optional
-Maintainer: Olivier Langella <olivier.langella at moulon.inra.fr>
-XSBC-Original-Maintainer: Olivier Langella <olivier.langella at moulon.inra.fr>
-Standards-Version: 1.2
-Build-Depends: debhelper (>= 5), cmake (>= 2), libqt4-dev (>= 4.5.2)
-Homepage: http://bioinformatics.org/~tryphon/populations/
-
-
-Package: populations
-Architecture: any
-Depends: ${shlibs:Depends}, libqt4-xml (>= 4.5.2)
-Description: population genetic software
- Populations is a population genetic software. It computes genetic distances between
- populations or individuals. It builds phylogenetic trees (NJ or UPGMA) with bootstrap values.
diff --git a/debian.orig/copyright b/debian.orig/copyright
deleted file mode 100644
index 4a015a4..0000000
--- a/debian.orig/copyright
+++ /dev/null
@@ -1,13 +0,0 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Olivier Langella <olivier.langella at moulon.inra.fr>
-X-Debianized-Date: Wed, 24 Oct 2001 11:18:51 +0200
-X-Source-Downloaded-From:
-X-Upstream-Author:
-
-Files: debian/*
-Copyright: © 2001 Olivier Langella <olivier.langella at moulon.inra.fr>
-License: GPL
-
-Files: *
-Copyright: © 2001 Olivier Langella <olivier.langella at moulon.inra.fr>
-License: GPL
diff --git a/debian.orig/rules b/debian.orig/rules
deleted file mode 100755
index c12a304..0000000
--- a/debian.orig/rules
+++ /dev/null
@@ -1,91 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-
-
-
-configure: configure-stamp
-configure-stamp:
- cmake -DCMAKE_INSTALL_PREFIX=/usr .
- dh_testdir
- # Add here commands to configure the package.
-
- touch configure-stamp
-
-
-build: build-stamp
-
-build-stamp: configure-stamp
- dh_testdir
-
- # Add here commands to compile the package.
- $(MAKE)
- #docbook-to-man debian/populations.sgml > populations.1
-
- touch $@
-
-clean:
- dh_testdir
- dh_testroot
- rm -f build-stamp configure-stamp CMakeCache.txt
-
- # Add here commands to clean up after the build process.
- -$(MAKE) clean
-
- dh_clean
-
-install: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
-
- # Add here commands to install the package into debian/populations.
- $(MAKE) DESTDIR=$(CURDIR)/debian/populations install
-
-
-# Build architecture-independent files here.
-binary-indep: build install
-# We have nothing to do by default.
-
-# Build architecture-dependent files here.
-binary-arch: build install
- dh_testdir
- dh_testroot
- dh_installchangelogs ChangeLog
- dh_installdocs
- dh_installexamples
-# dh_install
-# dh_installmenu
-# dh_installdebconf
-# dh_installlogrotate
-# dh_installemacsen
-# dh_installpam
-# dh_installmime
-# dh_python
-# dh_installinit
-# dh_installcron
-# dh_installinfo
- dh_installman
- dh_link
- dh_strip
- dh_compress
- dh_fixperms
-# dh_perl
-# dh_makeshlibs
- dh_installdeb
- dh_shlibdeps
- dh_gencontrol
- dh_md5sums
- dh_builddeb
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install configure
diff --git a/html/index.html b/html/index.html
index 1f6d05c..40b7214 100644
--- a/html/index.html
+++ b/html/index.html
@@ -1,268 +1,320 @@
<?xml version="1.0"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en">
- <head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/>
- <title>Populations </title>
- <link rel="stylesheet" href="./libcss/main.css" type="text/CSS"/>
- <!-- <link rel="shortcut icon" href="./libimage/icon.png" type="images/x-icon"/> -->
- </head>
- <body>
- <div>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<title>Populations</title>
+<link rel="stylesheet" href="./libcss/main.css" type="text/CSS" />
+<!-- <link rel="shortcut icon" href="./libimage/icon.png" type="images/x-icon"/> -->
+<script type="text/javascript">
+/* <![CDATA[ */
+ (function() {
+ var s = document.createElement('script'), t = document.getElementsByTagName('script')[0];
+
+ s.type = 'text/javascript';
+ s.async = true;
+ s.src = 'http://api.flattr.com/js/0.5.0/load.js?mode=auto';
+
+ t.parentNode.insertBefore(s, t);
+ })();
+/* ]]> */
+</script>
+</head>
+<body>
+<div>
- <h1>Populations 1.2.31</h1>
- <div class="paragraphe">Population genetic software (individuals or populations
- distances, phylogenetic trees)</div>
- <ul class="plan">
- <li>
- <a href="#ancre_fonctionnalites">Contents</a>
- </li>
- <li>
- <a href="#ancre_telechargement">Download</a>
- </li>
- <li>
- <a href="#ancre_distances">Distances</a>
- </li>
- <li>File <a href="#ancre_formats">formats</a></li>
- <li>
- <a href="#ancre_ligne_de_commande">Command line</a>
- </li>
- <li>
- <a href="#ancre_bibliographie">Bibliography</a>
- </li>
- <li>
- <a href="http://localhost/pge/bioinfo/populations/formules">Formula</a>
- </li>
- </ul>
+<h1>Populations 1.2.31</h1>
+<div class="paragraphe">Population genetic software (individuals
+or populations distances, phylogenetic trees)</div>
+<a class="FlattrButton" style="display:none;"
+href="http://bioinformatics.org/~tryphon/populations/"></a>
+<ul class="plan">
+ <li><a href="#ancre_fonctionnalites">Contents</a></li>
+ <li><a href="#ancre_telechargement">Download</a></li>
+ <li><a href="#ancre_distances">Distances</a></li>
+ <li>File <a href="#ancre_formats">formats</a></li>
+ <li><a href="#ancre_ligne_de_commande">Command line</a></li>
+ <li><a href="#ancre_bibliographie">Bibliography</a></li>
+ <li><a href="http://localhost/pge/bioinfo/populations/formules">Formula</a>
+ </li>
+</ul>
- <a id="ancre_fonctionnalites"/>
- <h2>Contents</h2>
- <ul class="enumeration">
- <li>haploids, diploids or polyploids genotypes (see input <a href="#ancre_formats"
- >formats</a>)</li>
- <li>structured populations (see input files <a href="#ancre_pop_struct">structured
- populations</a>
- </li>
- <li>No limit of populations, loci, alleles per loci (see input <a
- href="#ancre_formats">formats</a>) </li>
- <li>Distances between individuals (15 different <a href="#ancre_distances"
- >methods</a>)</li>
- <li>Distances between populations (15 <a href="#ancre_distances">methods</a>)</li>
- <li>Bootstraps on loci OR individuals</li>
- <li>Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA
- (PHYLIP tree format)</li>
- <li>Allelic diversity</li>
- <li>Converts data files from Genepop to different formats (Genepop, Genetix, Msat,
- Populations...)</li>
- </ul>
- <a id="ancre_telechargement"/>
- <h2>Download</h2>
- <div class="information">Populations, 1.2.30 Copyright (C) 1999, Olivier
- Langella, CNRS UPR9034 </div>
- <div class="paragraphe">This program is free software; you can redistribute it and/or
- modify it under the terms of the <a href="http://www.gnu.org/copyleft/gpl.html"> GNU
- General Public License</a> as published by the Free Software Foundation; either
- version 2 of the License, or (at your option) any later version licence</div>
- <div class="paragraphe">This program is distributed in the hope that it will be
- useful,but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the <a
- href="http://www.gnu.org/copyleft/gpl.html">GNU General Public License</a> for
- more details.</div>
- <div class="paragraphe">You should have received a copy of the GNU General Public
- License along with this program; if not, write to the Free Software Foundation,
- Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.</div>
- <div class="information">Authors</div>
- <div class="paragraphe">Olivier Langella</div>
- <div class="paragraphe">
- <h3>all systems</h3>
- <a
- href="http://bioinformatics.org/project/?group_id=84"
- >download populations</a>
-
- </div>
- <div class="paragraphe">
- <h3>Ubuntu packages</h3>
- If you are using Ubuntu, you can find "populations" and "treeplot" packages here :<br/>
- <a href="https://launchpad.net/~olivier-langella/+archive">
- https://launchpad.net/~olivier-langella/+archive</a><br/>
- Please modify your source list entries to add the repositorie that corresponds to your Ubuntu version (
- <a href="https://help.ubuntu.com/community/Repositories/Ubuntu#Adding%20Repositories%20in%20Ubuntu">
- Adding Repositories in Ubuntu how to</a>
- )
-
- </div>
- <a id="ancre_distances"/>
- <h2>Distances</h2>
- <ul class="enumeration">
- <li>
- <a href="./formules/das.xhtml">DAS,
- shared allele distance</a> (Chakraborty et Jin., 1993)</li>
- <li><a href="./formules/nei_ds.xhtml">Nei, minimum genetic distance</a>, Dm (Nei,1987)</li>
- <li><a href="./formules/nei_dm.xhtml">Nei, standard genetic distance</a>, Ds (Nei, 1987)</li>
- <li><a href="./formules/cavali_sforza.xhtml">Cavalli-Sforza and Edwards</a>, Dc (1967)</li>
- <li><a href="./formules/nei_da.xhtml">Nei et al's</a>, D<sub>A</sub> (1983)</li>
- <li><a href="./formules/latter_fst.xhtml">Latter</a>, Fst (1972)</li>
- <li><a href="./formules/prevosti.xhtml">Prevosti et al.'s</a>, Cp (1975)</li>
- <li><a href="./formules/roger.xhtml">Roger's</a>, Dr (1972)</li>
- <li><a href="./formules/reynold_dru.xhtml">Reynolds J. unweighted</a>, Dru (1983)</li>
- <li><a href="./formules/reynold_drw.xhtml">Reynolds J. weighted</a>, Drw (1983)</li>
- <li><a href="./formules/reynold_least_square.xhtml">Reynolds J. least squares</a>, Drl (1983)</li>
- <li>Microsatellites distances</li>
- <li>Goldstein et al., dmu2 (1995a)</li>
- <li>Average Square Distance ( ASD , Goldstein, Slatkin 1995)</li>
- <li>Shriver et al's, Dsw (1995)</li>
- <li>Lev A. Zhivotovsky, DR (1999)
- </li>
- </ul>
- <a id="ancre_formats"/>
- <h2>Formats</h2>
- <div class="plan">- <a href="#ancre_formats_entree">input</a></div>
- <div class="plan">- <a href="#ancre_formats_sortie">output</a></div>
- <a id="ancre_formats_entree"/>
- <h3>input files</h3>
- <div class="paragraphe">"Populations" accepts file from other population genetic
- softwares:</div>
- <div class="enumeration">- <a href="http://www.cefe.cnrs-mop.fr/">Genepop</a></div>
- <div class="enumeration">- <a
- href="http://www.univ-montp2.fr/%7Egenetix/genetix/genetix.htm">Génétix</a>
- </div>
- <div class="paragraphe"> and it has its own format:<br/>"Populations" format allows to
- use unlimited number of alleles, of haploids, diploids or nploids. The format is
- close to Genepop but alleles at a given locus are separated by ":". Thus, man can
- code alleles with all ASCII characters.</div>
- <div class="paragraphe">Diploid population example:</div>
- <div class="script"> "Grape populations in southern France"<br/> ADHLocus1<br/>
- ADH#2<br/> ADHthree<br/> ADH-4<br/> ADH-5<br/> Pop Montpellier<br/> Montpellier1 ,
- 02:01 03:03 01:02 03:02 10:11<br/> Montpellier2 , 02:02 03:01 01:02 03:03 11:11<br/>
- Montpellier3 , 01:02 04:01 02:02 01:02 10:10<br/> Montpellier4 , 01:03 02:02 01:01
- 02:02 10:11<br/> Montpellier5 , 02:03 02:04 01:01 01:02 10:10<br/> POP Gigondas<br/>
- Gigondas1 , 01:02 02:02 02:01 04:05 08:07<br/> Gigondas2 , 01:02 02:01 02:01 04:05
- 03:07<br/> Gigondas3 , 02:01 02:03 01:01 05:05 04:02<br/> Gigondas4 , 02:01 03:03
- 03:01 03:03 06:03<br/> Gigondas5 , 01:01 02:01 03:01 05:05 08:07<br/>
- </div>
+<a id="ancre_fonctionnalites" />
+<h2>Contents</h2>
+<ul class="enumeration">
+ <li>haploids, diploids or polyploids genotypes (see input <a
+ href="#ancre_formats">formats</a>)</li>
+ <li>structured populations (see input files <a
+ href="#ancre_pop_struct">structured populations</a></li>
+ <li>No limit of populations, loci, alleles per loci (see input <a
+ href="#ancre_formats">formats</a>)</li>
+ <li>Distances between individuals (15 different <a
+ href="#ancre_distances">methods</a>)</li>
+ <li>Distances between populations (15 <a href="#ancre_distances">methods</a>)</li>
+ <li>Bootstraps on loci OR individuals</li>
+ <li>Phylogenetic trees (individuals or populations), using
+ Neighbor Joining or UPGMA (PHYLIP tree format)</li>
+ <li>Allelic diversity</li>
+ <li>Converts data files from Genepop to different formats
+ (Genepop, Genetix, Msat, Populations...)</li>
+</ul>
+<a id="ancre_telechargement" />
+<h2>Download</h2>
+<div class="information">Populations, 1.2.30 Copyright (C) 1999,
+Olivier Langella, CNRS UPR9034</div>
+<div class="paragraphe">This program is free software; you can
+redistribute it and/or modify it under the terms of the <a
+ href="http://www.gnu.org/copyleft/gpl.html"> GNU General Public
+License</a> as published by the Free Software Foundation; either version 2
+of the License, or (at your option) any later version licence</div>
+<div class="paragraphe">This program is distributed in the hope
+that it will be useful,but WITHOUT ANY WARRANTY; without even the
+implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+See the <a href="http://www.gnu.org/copyleft/gpl.html">GNU General
+Public License</a> for more details.</div>
+<div class="paragraphe">You should have received a copy of the GNU
+General Public License along with this program; if not, write to the
+Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
+02111-1307, USA.</div>
+<div class="information">Authors</div>
+<div class="paragraphe">Olivier Langella</div>
+<div class="paragraphe">
+<h3>all systems</h3>
+<a href="http://bioinformatics.org/project/?group_id=84">download
+populations</a></div>
+<div class="paragraphe">
+<h3>Ubuntu packages</h3>
+If you are using Ubuntu, you can find "populations" and "treeplot"
+packages here :<br />
+<a href="https://launchpad.net/~olivier-langella/+archive">
+https://launchpad.net/~olivier-langella/+archive</a><br />
+Please modify your source list entries to add the repositorie that
+corresponds to your Ubuntu version ( <a
+ href="https://help.ubuntu.com/community/Repositories/Ubuntu#Adding%20Repositories%20in%20Ubuntu">
+Adding Repositories in Ubuntu how to</a> )</div>
+<a id="ancre_distances" />
+<h2>Distances</h2>
+<ul class="enumeration">
+ <li><a href="./formules/das.xhtml">DAS, shared allele distance</a>
+ (Chakraborty et Jin., 1993)</li>
+ <li><a href="./formules/nei_ds.xhtml">Nei, minimum genetic
+ distance</a>, Dm (Nei,1987)</li>
+ <li><a href="./formules/nei_dm.xhtml">Nei, standard genetic
+ distance</a>, Ds (Nei, 1987)</li>
+ <li><a href="./formules/cavali_sforza.xhtml">Cavalli-Sforza
+ and Edwards</a>, Dc (1967)</li>
+ <li><a href="./formules/nei_da.xhtml">Nei et al's</a>, D<sub>A</sub>
+ (1983)</li>
+ <li><a href="./formules/latter_fst.xhtml">Latter</a>, Fst (1972)</li>
+ <li><a href="./formules/prevosti.xhtml">Prevosti et al.'s</a>, Cp
+ (1975)</li>
+ <li><a href="./formules/roger.xhtml">Roger's</a>, Dr (1972)</li>
+ <li><a href="./formules/reynold_dru.xhtml">Reynolds J.
+ unweighted</a>, Dru (1983)</li>
+ <li><a href="./formules/reynold_drw.xhtml">Reynolds J.
+ weighted</a>, Drw (1983)</li>
+ <li><a href="./formules/reynold_least_square.xhtml">Reynolds
+ J. least squares</a>, Drl (1983)</li>
+ <li>Microsatellites distances</li>
+ <li>Goldstein et al., dmu2 (1995a)</li>
+ <li>Average Square Distance ( ASD , Goldstein, Slatkin 1995)</li>
+ <li>Shriver et al's, Dsw (1995)</li>
+ <li>Lev A. Zhivotovsky, DR (1999)</li>
+</ul>
+<a id="ancre_formats" />
+<h2>Formats</h2>
+<div class="plan">- <a href="#ancre_formats_entree">input</a></div>
+<div class="plan">- <a href="#ancre_formats_sortie">output</a></div>
+<a id="ancre_formats_entree" />
+<h3>input files</h3>
+<div class="paragraphe">"Populations" accepts file from other
+population genetic softwares:</div>
+<div class="enumeration">- <a href="http://www.cefe.cnrs-mop.fr/">Genepop</a></div>
+<div class="enumeration">- <a
+ href="http://www.univ-montp2.fr/%7Egenetix/genetix/genetix.htm">Génétix</a>
+</div>
+<div class="paragraphe">and it has its own format:<br />
+"Populations" format allows to use unlimited number of alleles, of
+haploids, diploids or nploids. The format is close to Genepop but
+alleles at a given locus are separated by ":". Thus, man can code
+alleles with all ASCII characters.</div>
+<div class="paragraphe">Diploid population example:</div>
+<div class="script">"Grape populations in southern France"<br />
+ADHLocus1<br />
+ADH#2<br />
+ADHthree<br />
+ADH-4<br />
+ADH-5<br />
+Pop Montpellier<br />
+Montpellier1 , 02:01 03:03 01:02 03:02 10:11<br />
+Montpellier2 , 02:02 03:01 01:02 03:03 11:11<br />
+Montpellier3 , 01:02 04:01 02:02 01:02 10:10<br />
+Montpellier4 , 01:03 02:02 01:01 02:02 10:11<br />
+Montpellier5 , 02:03 02:04 01:01 01:02 10:10<br />
+POP Gigondas<br />
+Gigondas1 , 01:02 02:02 02:01 04:05 08:07<br />
+Gigondas2 , 01:02 02:01 02:01 04:05 03:07<br />
+Gigondas3 , 02:01 02:03 01:01 05:05 04:02<br />
+Gigondas4 , 02:01 03:03 03:01 03:03 06:03<br />
+Gigondas5 , 01:01 02:01 03:01 05:05 08:07<br />
+</div>
- <div class="paragraphe">Haploid example :</div>
- <div class="script"> "Grape populations in southern France"<br/> ADHLocus1<br/>
- ADH#2<br/> ADHthree<br/> ADH-4<br/> ADH-5<br/> Pop Montpellier<br/> Montpellier1 ,
- 02 03 01 03 10<br/> Montpellier2 , 02 03 01 03 11<br/> Montpellier3 , 01 04 02 01
- 10<br/> Montpellier4 , 01 02 01 02 10<br/> Montpellier5 , 02 02 01 01 10<br/> POP
- Gigondas<br/> Gigondas1 , 01 02 02 04 08<br/> Gigondas2 , 01 02 02 04 03<br/>
- Gigondas3 , 02 02 01 05 04<br/> Gigondas4 , 02 03 03 03 06<br/> Gigondas5 , 01 02 03
- 05 08<br/>
- </div>
+<div class="paragraphe">Haploid example :</div>
+<div class="script">"Grape populations in southern France"<br />
+ADHLocus1<br />
+ADH#2<br />
+ADHthree<br />
+ADH-4<br />
+ADH-5<br />
+Pop Montpellier<br />
+Montpellier1 , 02 03 01 03 10<br />
+Montpellier2 , 02 03 01 03 11<br />
+Montpellier3 , 01 04 02 01 10<br />
+Montpellier4 , 01 02 01 02 10<br />
+Montpellier5 , 02 02 01 01 10<br />
+POP Gigondas<br />
+Gigondas1 , 01 02 02 04 08<br />
+Gigondas2 , 01 02 02 04 03<br />
+Gigondas3 , 02 02 01 05 04<br />
+Gigondas4 , 02 03 03 03 06<br />
+Gigondas5 , 01 02 03 05 08<br />
+</div>
- <div class="paragraphe">example of haploid, using any ASCII character: no space in
- allele names:</div>
- <div class="script"> "Grape populations in southern France"<br/> ADHLocus1<br/>
- ADH#2<br/> ADHthree<br/> ADH-4<br/> ADH-5<br/> Pop Montpellier<br/> Montpellier1 ,
- all2 03 01 03 10<br/> Montpellier2 , all2 03 01 03 11<br/> Montpellier3 , all1 04 02
- 01 miss<br/> Montpellier4 , all1 02 01 02 10<br/> Montpellier5 , all2 02 01 01
- 10<br/> POP Gigondas<br/> Gigondas1 , all1 02 02 04 08<br/> Gigondas2 , all1 02 02
- 04 miss<br/> Gigondas3 , all2 02 01 05 04<br/> Gigondas4 , all2 03 03 03 06<br/>
- Gigondas5 , all1 02 03 05 08<br/>
- </div>
+<div class="paragraphe">example of haploid, using any ASCII
+character: no space in allele names:</div>
+<div class="script">"Grape populations in southern France"<br />
+ADHLocus1<br />
+ADH#2<br />
+ADHthree<br />
+ADH-4<br />
+ADH-5<br />
+Pop Montpellier<br />
+Montpellier1 , all2 03 01 03 10<br />
+Montpellier2 , all2 03 01 03 11<br />
+Montpellier3 , all1 04 02 01 miss<br />
+Montpellier4 , all1 02 01 02 10<br />
+Montpellier5 , all2 02 01 01 10<br />
+POP Gigondas<br />
+Gigondas1 , all1 02 02 04 08<br />
+Gigondas2 , all1 02 02 04 miss<br />
+Gigondas3 , all2 02 01 05 04<br />
+Gigondas4 , all2 03 03 03 06<br />
+Gigondas5 , all1 02 03 05 08<br />
+</div>
- <a id="ancre_pop_struct"/>
- <h3>Structured population</h3>
- <div class="paragraphe">To code metapopulations, you can choose either "Genepop" or
- "Populations" format. You only need to give the name of population after the keyword
- "POP " (separator = "/")</div>
- <div class="paragraphe">example:</div>
- <div class="script"> exemple de populations structurées<br/> locus1<br/> locus2<br/>
- locus3<br/> POP Rennes/immeuble_sud/pop_3emeetage<br/> ind1, (description des
- individus)<br/> ind2, ...<br/> ind3, ...<br/> ind4, ...<br/> POP
- Rennes/immeuble_sud/pop_2emeetage<br/> ind1, (description des individus)<br/> ind2,
- ...<br/> ind3, ...<br/> ind4, ...<br/>
- </div>
+<a id="ancre_pop_struct" />
+<h3>Structured population</h3>
+<div class="paragraphe">To code metapopulations, you can choose
+either "Genepop" or "Populations" format. You only need to give the name
+of population after the keyword "POP " (separator = "/")</div>
+<div class="paragraphe">example:</div>
+<div class="script">exemple de populations structurées<br />
+locus1<br />
+locus2<br />
+locus3<br />
+POP Rennes/immeuble_sud/pop_3emeetage<br />
+ind1, (description des individus)<br />
+ind2, ...<br />
+ind3, ...<br />
+ind4, ...<br />
+POP Rennes/immeuble_sud/pop_2emeetage<br />
+ind1, (description des individus)<br />
+ind2, ...<br />
+ind3, ...<br />
+ind4, ...<br />
+</div>
- <a id="ancre_formats_sortie"/>
- <h3>Output files</h3>
- <div class="paragraphe">Populations is able to produce various population genetic
- software formats:</div>
- <div class="enumeration">
- <a href="http://www.cefe.cnrs-mop.fr/">Genepop</a>
- </div>
- <div class="enumeration">
- <a href="http://www.univ-montp2.fr/%7Egenetix/genetix/genetix.htm">Génétix</a>
- </div>
- <div class="enumeration">Populations</div>
- <div class="enumeration">
- Lea
- </div>
- <div class="enumeration">
- <a href="http://www.rannala.org/docs/immanc.html">Immanc</a>
- </div>
- <div class="enumeration">microsat</div>
- <div class="enumeration">
- <a href="http://www.unife.it/genetica/Giorgio/giorgio_soft.html#ADMIX">Admix (G.
- Bertorelle)</a>
- </div>
- <div class="enumeration">
- <a href="http://www.unil.ch/izea/softwares/fstat.html">Fstat (Jerome Goudet)</a>
- </div>
- <div class="paragraphe">Phylogenetic trees are coded using the "Phylip" format. " <a
- href="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html">Treeview</a>" can be
- used for Windows or Linux, and you can use ">Treeplot" to
- convert the phylip format into postscript, adobe illustrator, gif... with colors for
- each populations</div>
- <div class="paragraphe">Matrix distances files are "Excel (gnumeric compatible)",
- "Phylip", "xgobi", "NTsys" or any text editor compliant.</div>
- <a id="ancre_ligne_de_commande"/>
- <h3>Command line</h3>
- <div class="paragraphe">You can use "Populations" as a command line programm (very
- useful for batch treatment) to infer phylogenetic trees:</div>
- <div class="commande">populations name_of_input_file -"arguments"</div>
- <div class="paragraphe">Available arguments:</div>
- <div class="enumeration">-phylogeny ind ou pop (default) for phylogenetic trees based on
- individuals or populations</div>
- <div class="enumeration">-dist method (default: Nei standard, Ds) you can choose among:
- DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw, Dr, Dru, Drw, Drl. see distances
- for details.</div>
- <div class="enumeration">-construct method (default: upgma) possibilities upgma or nj
- (Neighbor Joining)</div>
- <div class="enumeration">-bootstrap_ind number to indicate the number of bootstraps to
- perform on individuals</div>
- <div class="enumeration">-bootstrap_locus number to indicate the number of bootstraps to
- perform on loci</div>
- <div class="enumeration">-output name_of_treeview_file to indicate the name of the tree
- file (phylip tree format)</div>
- <div class="enumeration">-level number , structured populations allows to choose the
- structuration factor (in the example: town level is 1, building level is 2...).</div>
- <div class="paragraphe">example:</div>
- <div class="script">populations toutc2.txt -phylogeny pop -dist Dm -bootstrap_locus
- 10000 -output toutc2_10000_Dm.tre</div>
- <div class="paragraphe">Commands can be write in a .bat file (for DOS) or a script file
- (for UNIX).</div>
- <a id="ancre_bibliographie"/>
- <h2>Bibliography</h2>
- <div class="article"><strong>Bruce Ranala and Joanna L. Mountain.</strong> Detecting
- immigration by using multilocus genotypes. Proc.Natl. Acad. Sci. USA, 94:9197-9201,
- 13/6/1997. </div>
- <div class="article"><strong>David B. Goldstein, Andres Ruiz Linares, Luigi Luca
- Cavalli-Sforza and Marcus W. Feldman.</strong> An Evaluation of Genetic
- Distances for Use With Microsatellite Loci. Genetics, 139:463-471, 5/10/1994. </div>
- <div class="article"><strong>D. B. Goldstein and D. D. Pollock.</strong> Launching
- Microsatellites: A Review of Mutation Processes and Methods of Phylogenetic
- Inference. Journal of Heredity, 88(335-342):0022-1503, 31/3/1997. </div>
- <div class="article" id="pubdas"><strong>Li Jin and Ranajit Chakraborty.</strong> Estimation of
- Genetic Distance and Coefficient of Gene Diversity from Single-Probe Multilocus DNA
- Fingerprinting Data. Mol. Biol. Evol, 11(1):120-127, 13/9/1993. </div>
- <div class="article"><strong>Mark D. Shriver, Li Jin, Eric Boerwinkle, Ranjan Deka,
- Robert E. Ferrel and Ranajit Chakraborty.</strong> A Novel Measure of Genetic
- Distance for Highly Polymorphic Tandem Repeat Loci. Mol. Biol. Evol, 12(5):914-920,
- 13/4/1995. </div>
- <div class="article"><strong>Montgomery Slatkin.</strong> A Measure of Population
- Subdivision on Microsatellite Allele Frequencies. Genetics, (139):457-462,
- 19/6/1994. </div>
- <div class="article"><strong>Naruya Saitou and Masatoshi Nei.</strong> The
- Neigbhor-joining Method: A New Method for Reconstructing Phylogenetic Trees. Mol.
- Biol. Evol, 4(4):406-425, 18/2/1987. </div>
- <div class="article"><strong>Naoko Takezaki and Masatoshi Nei.</strong> Genetic
- Distances and Reconstruction of Phylogenetic Trees From Microsatellite DNA.
- Genetics, (144):189-399, 6/6/1996. </div>
- <div class="article"><strong>William J. Bruno, Nicholas D. Socci and Aaron L.
- Halpern.</strong> Weighted Neigbhor Joining: A Likelihood-Based Approach to
- Distance-Based Phylogeny Reconstruction. Mol. Biol. Evol, 17(1):189-197, 11/10/1999. </div>
+<a id="ancre_formats_sortie" />
+<h3>Output files</h3>
+<div class="paragraphe">Populations is able to produce various
+population genetic software formats:</div>
+<div class="enumeration"><a href="http://www.cefe.cnrs-mop.fr/">Genepop</a>
+</div>
+<div class="enumeration"><a
+ href="http://www.univ-montp2.fr/%7Egenetix/genetix/genetix.htm">Génétix</a>
+</div>
+<div class="enumeration">Populations</div>
+<div class="enumeration">Lea</div>
+<div class="enumeration"><a
+ href="http://www.rannala.org/docs/immanc.html">Immanc</a></div>
+<div class="enumeration">microsat</div>
+<div class="enumeration"><a
+ href="http://www.unife.it/genetica/Giorgio/giorgio_soft.html#ADMIX">Admix
+(G. Bertorelle)</a></div>
+<div class="enumeration"><a
+ href="http://www.unil.ch/izea/softwares/fstat.html">Fstat (Jerome
+Goudet)</a></div>
+<div class="paragraphe">Phylogenetic trees are coded using the
+"Phylip" format. " <a
+ href="http://taxonomy.zoology.gla.ac.uk/rod/treeview.html">Treeview</a>"
+can be used for Windows or Linux, and you can use ">Treeplot" to convert
+the phylip format into postscript, adobe illustrator, gif... with colors
+for each populations</div>
+<div class="paragraphe">Matrix distances files are "Excel
+(gnumeric compatible)", "Phylip", "xgobi", "NTsys" or any text editor
+compliant.</div>
+<a id="ancre_ligne_de_commande" />
+<h3>Command line</h3>
+<div class="paragraphe">You can use "Populations" as a command
+line programm (very useful for batch treatment) to infer phylogenetic
+trees:</div>
+<div class="commande">populations name_of_input_file -"arguments"</div>
+<div class="paragraphe">Available arguments:</div>
+<div class="enumeration">-phylogeny ind ou pop (default) for
+phylogenetic trees based on individuals or populations</div>
+<div class="enumeration">-dist method (default: Nei standard, Ds)
+you can choose among: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw,
+Dr, Dru, Drw, Drl. see distances for details.</div>
+<div class="enumeration">-construct method (default: upgma)
+possibilities upgma or nj (Neighbor Joining)</div>
+<div class="enumeration">-bootstrap_ind number to indicate the
+number of bootstraps to perform on individuals</div>
+<div class="enumeration">-bootstrap_locus number to indicate the
+number of bootstraps to perform on loci</div>
+<div class="enumeration">-output name_of_treeview_file to indicate
+the name of the tree file (phylip tree format)</div>
+<div class="enumeration">-level number , structured populations
+allows to choose the structuration factor (in the example: town level is
+1, building level is 2...).</div>
+<div class="paragraphe">example:</div>
+<div class="script">populations toutc2.txt -phylogeny pop -dist Dm
+-bootstrap_locus 10000 -output toutc2_10000_Dm.tre</div>
+<div class="paragraphe">Commands can be write in a .bat file (for
+DOS) or a script file (for UNIX).</div>
+<a id="ancre_bibliographie" />
+<h2>Bibliography</h2>
+<div class="article"><strong>Bruce Ranala and Joanna L.
+Mountain.</strong> Detecting immigration by using multilocus genotypes.
+Proc.Natl. Acad. Sci. USA, 94:9197-9201, 13/6/1997.</div>
+<div class="article"><strong>David B. Goldstein, Andres
+Ruiz Linares, Luigi Luca Cavalli-Sforza and Marcus W. Feldman.</strong> An
+Evaluation of Genetic Distances for Use With Microsatellite Loci.
+Genetics, 139:463-471, 5/10/1994.</div>
+<div class="article"><strong>D. B. Goldstein and D. D.
+Pollock.</strong> Launching Microsatellites: A Review of Mutation Processes and
+Methods of Phylogenetic Inference. Journal of Heredity,
+88(335-342):0022-1503, 31/3/1997.</div>
+<div class="article" id="pubdas"><strong>Li Jin and
+Ranajit Chakraborty.</strong> Estimation of Genetic Distance and Coefficient of
+Gene Diversity from Single-Probe Multilocus DNA Fingerprinting Data.
+Mol. Biol. Evol, 11(1):120-127, 13/9/1993.</div>
+<div class="article"><strong>Mark D. Shriver, Li Jin,
+Eric Boerwinkle, Ranjan Deka, Robert E. Ferrel and Ranajit Chakraborty.</strong>
+A Novel Measure of Genetic Distance for Highly Polymorphic Tandem Repeat
+Loci. Mol. Biol. Evol, 12(5):914-920, 13/4/1995.</div>
+<div class="article"><strong>Montgomery Slatkin.</strong> A
+Measure of Population Subdivision on Microsatellite Allele Frequencies.
+Genetics, (139):457-462, 19/6/1994.</div>
+<div class="article"><strong>Naruya Saitou and Masatoshi
+Nei.</strong> The Neigbhor-joining Method: A New Method for Reconstructing
+Phylogenetic Trees. Mol. Biol. Evol, 4(4):406-425, 18/2/1987.</div>
+<div class="article"><strong>Naoko Takezaki and Masatoshi
+Nei.</strong> Genetic Distances and Reconstruction of Phylogenetic Trees From
+Microsatellite DNA. Genetics, (144):189-399, 6/6/1996.</div>
+<div class="article"><strong>William J. Bruno, Nicholas
+D. Socci and Aaron L. Halpern.</strong> Weighted Neigbhor Joining: A
+Likelihood-Based Approach to Distance-Based Phylogeny Reconstruction.
+Mol. Biol. Evol, 17(1):189-197, 11/10/1999.</div>
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diff --git a/html/old_formula/WARNINGS b/html/old_formula/WARNINGS
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+No implementation found for style `fontenc'
+
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diff --git a/html/old_formula/formules.css b/html/old_formula/formules.css
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+/* Century Schoolbook font is very similar to Computer Modern Math: cmmi */
+.MATH { font-family: "Century Schoolbook", serif; }
+.MATH I { font-family: "Century Schoolbook", serif; font-shape: italic }
+.BOLDMATH { font-family: "Century Schoolbook", serif; font-weight: bold }
+
+/* implement both fixed-size and relative sizes */
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+/* heading styles */
+H1 { }
+H2 { }
+H3 { }
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+H5 { }
+
+/* mathematics styles */
+DIV.displaymath { } /* math displays */
+TD.eqno { } /* equation-number cells */
+
+
+/* document-specific styles come next */
diff --git a/html/old_formula/formules.html b/html/old_formula/formules.html
new file mode 100755
index 0000000..7947cf5
--- /dev/null
+++ b/html/old_formula/formules.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>formules</TITLE>
+<META NAME="description" CONTENT="formules">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html2"
+ HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up_g.png">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev_g.png">
+<BR>
+<B> Next:</B> <A NAME="tex2html3"
+ HREF="node1.html">Distances</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html4"
+ HREF="node1.html">Distances</A>
+<UL>
+<LI><A NAME="tex2html5"
+ HREF="node2.html">IAM distances</A>
+<UL>
+<LI><A NAME="tex2html6"
+ HREF="node3.html">Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]</A>
+<LI><A NAME="tex2html7"
+ HREF="node4.html">Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html8"
+ HREF="node5.html">Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html9"
+ HREF="node6.html">Latter's (1972) Fst (=<IMG
+ WIDTH="14" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img16.png"
+ ALT="\( \phi \protect \)">*) distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html10"
+ HREF="node7.html">Rogers' (1972) distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html11"
+ HREF="node8.html">Prevosti et al's (1975) distance [Takezaki, N. 96] has a statistical property
+similar to that of Dr and is defined as</A>
+<LI><A NAME="tex2html12"
+ HREF="node9.html">Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html13"
+ HREF="node10.html">Nei et al's (1983) <IMG
+ WIDTH="28" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img21.png"
+ ALT="\( D_{A}\protect \)"> distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html14"
+ HREF="node11.html">Sanghvi's (1953) <IMG
+ WIDTH="26" HEIGHT="16" ALIGN="BOTTOM" BORDER="0"
+ SRC="img23.png"
+ ALT="\( X^{2}\protect \)"> distance[Takezaki, N. 96]</A>
+<LI><A NAME="tex2html15"
+ HREF="node12.html">Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]</A>
+<UL>
+<LI><A NAME="tex2html16"
+ HREF="node13.html">unweighted average of single-locus ratio estimators, <!-- MATH
+ $\tilde{\theta }_{U}\protect$
+ -->
+<IMG
+ WIDTH="22" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img30.png"
+ ALT="\( \tilde{\theta }_{U}\protect \)">:</A>
+<LI><A NAME="tex2html17"
+ HREF="node14.html">weighted average of single-locus ratio estimators :</A>
+<LI><A NAME="tex2html18"
+ HREF="node15.html">least squares <!-- MATH
+ $\theta \protect$
+ -->
+<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="\( \theta \)"> estimator :</A>
+</UL>
+</UL>
+<LI><A NAME="tex2html19"
+ HREF="node16.html">SMM distances</A>
+<UL>
+<LI><A NAME="tex2html20"
+ HREF="node17.html">Goldstein et al. (1995a) [Goldstein, D.B. 97]</A>
+<LI><A NAME="tex2html21"
+ HREF="node18.html">average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995)
+[Goldstein, D.B. 97]</A>
+<LI><A NAME="tex2html22"
+ HREF="node19.html">Shriver et al.'s (1995) [Shriver, M.D. 95]</A>
+<LI><A NAME="tex2html23"
+ HREF="node20.html">Lev A. Zhivotovsky (1999) [Takezaki, N. 96]</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html24"
+ HREF="node21.html">Bibliography</A>
+<LI><A NAME="tex2html25"
+ HREF="node22.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/images.aux b/html/old_formula/images.aux
new file mode 100755
index 0000000..78ebd78
--- /dev/null
+++ b/html/old_formula/images.aux
@@ -0,0 +1,5 @@
+\relax
+\select at language{english}
+\@writefile{toc}{\select at language{english}}
+\@writefile{lof}{\select at language{english}}
+\@writefile{lot}{\select at language{english}}
diff --git a/html/old_formula/images.bbl b/html/old_formula/images.bbl
new file mode 100755
index 0000000..52213c2
--- /dev/null
+++ b/html/old_formula/images.bbl
@@ -0,0 +1,38 @@
+\begin{thebibliography}{{Goldstein, D.B.}~97}
+
+\bibitem[{Goldstein, D.B.}~97]{GP97}
+{Goldstein, D.B.} \& {Pollock, D.D.}
+\newblock {\em Launching Microsatellites: A Review of Mutation Processes and
+ Methods of Phylogenetic Inference}.
+\newblock Journal of Heredity, vol.~88, no.~335-342, pages 0022--1503, 31 1997.
+\newblock 1997.
+
+\bibitem[{Jin, L.}~93]{JC93}
+{Jin, L.} \& {Chakraborty, R.}
+\newblock {\em Estimation of {G}enetic {D}istance and {C}oefficient of {G}ene
+ {D}iversity from {S}ingle-{P}robe {M}ultilocus {DNA} {F}ingerprinting
+ {D}ata}.
+\newblock Mol. Biol. Evol., vol.~11, no.~1, pages 120--127, 13 1993.
+\newblock 1994.
+
+\bibitem[{Reynolds, J.}~83]{RWC83}
+{Reynolds, J.}, {Weir, B.S.} \& {Cockerham, C.}
+\newblock {\em Estimation of the coancestry coefficient: basis for a short-term
+ genetic distance}.
+\newblock Genetics Society of America, vol.~105, pages 767--779, November 1983.
+\newblock 1983.
+
+\bibitem[{Shriver, M.D.}~95]{SJB95}
+{Shriver, M.D.}, {Jin, L.} \& {Boerwinkle, E.}
+\newblock {\em A Novel Measure of Genetic Distance for Highly Polymorphic
+ Tandem Repeat Loci}.
+\newblock Mol. Bio. Evol., vol.~12, no.~5, pages 914--920, 4 1995.
+
+\bibitem[{Takezaki, N.}~96]{TN96}
+{Takezaki, N.} \& {Nei, M.}
+\newblock {\em Genetic {D}istances and {R}econstruction of {P}hylogenetic
+ {T}rees {F}rom {M}icrosatellite {DNA}}.
+\newblock Genetics, no.~144, pages 189--399, 6 1996.
+\newblock september, 1996.
+
+\end{thebibliography}
diff --git a/html/old_formula/images.pl b/html/old_formula/images.pl
new file mode 100755
index 0000000..ab33bdb
--- /dev/null
+++ b/html/old_formula/images.pl
@@ -0,0 +1,410 @@
+# LaTeX2HTML 2K.1beta (1.48)
+# Associate images original text with physical files.
+
+
+$key = q/(y_{ij});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="23" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img6.png"
+ ALT="\( y_{ij} \)">|;
+
+$key = q/{displaymath}a_{l}=frac{1}{2}sum_{u}left(tilde{p}_{1lu}-tilde{p}_{2lu}right)^{2}alpha}_{2l}right)}{4n_{1}n_{2}left(n_{1}+n_{2}-1right)}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="364" HEIGHT="49" BORDER="0"
+ SRC="|."$dir".q|img35.png"
+ ALT="\begin{displaymath}
+a_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{...
+...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}">|;
+
+$key = q/{displaymath}Ds=-lnleft[frac{J_{XY}}{sqrt{J_{X}J_{Y}}}right]{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="144" HEIGHT="45" BORDER="0"
+ SRC="|."$dir".q|img14.png"
+ ALT="\begin{displaymath}
+Ds=-\ln \left[ \frac{J_{XY}}{\sqrt{J_{X}J_{Y}}}\right] \end{displaymath}">|;
+
+$key = q/(n_{c}=frac{left(rbar{n}-sum^{r}_{i=1}frac{n^{2}_{i}}{rbar{n}}right)}{left(r-1right)});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="143" HEIGHT="74" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img27.png"
+ ALT="\( n_{c}=\frac{\left( r\bar{n}-\sum ^{r}_{i=1}\frac{n^{2}_{i}}{r\bar{n}}\right) }{\left( r-1\right) } \)">|;
+
+$key = q/{displaymath}R=frac{left(2x+y+zright)tilde{theta}_{L}^{2}-2left(x+zright)tilde{theta}_{L}+z}{1-2tilde{theta}_{L}+2tilde{theta}_{L}^{2}}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="266" HEIGHT="50" BORDER="0"
+ SRC="|."$dir".q|img43.png"
+ ALT="\begin{displaymath}
+R=\frac{\left( 2x+y+z\right) \tilde{\theta }_{L}^{2}-2\left(...
+...theta }_{L}+z}{1-2\tilde{\theta }_{L}+2\tilde{\theta }_{L}^{2}}\end{displaymath}">|;
+
+$key = q/(X^{2});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="26" HEIGHT="16" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img23.png"
+ ALT="\( X^{2}\protect \)">|;
+
+$key = q/{displaymath}X^{2}=frac{sum^{r}_{j}sum^{m_{j}}_{i}2frac{left(x_{ij}-y_{ij}right)^{2}}{left(x_{ij}+y_{ij}right)}}{r}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="180" HEIGHT="50" BORDER="0"
+ SRC="|."$dir".q|img24.png"
+ ALT="\begin{displaymath}
+X^{2}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}2\frac{\left( x_{ij}-y_{ij}\right) ^{2}}{\left( x_{ij}+y_{ij}\right) }}{r}\end{displaymath}">|;
+
+$key = q/(tilde{theta}_{l}=frac{a_{l}}{a_{l}+b_{l}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="73" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img32.png"
+ ALT="\( \tilde{\theta }_{l}=\frac{a_{l}}{a_{l}+b_{l}} \)">|;
+
+$key = q/{displaymath}DReynold=-ln(1-theta){displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="168" HEIGHT="28" BORDER="0"
+ SRC="|."$dir".q|img25.png"
+ ALT="\begin{displaymath}
+DReynold=-\ln (1-\theta )\end{displaymath}">|;
+
+$key = q/{displaymath}Dc=frac{2}{Pir}sum^{r}_{j}sqrt{2left((1-sum_{i}^{m_{j}}sqrt{x_{ij}y_{ij}}right)}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="258" HEIGHT="64" BORDER="0"
+ SRC="|."$dir".q|img20.png"
+ ALT="\begin{displaymath}
+Dc=\frac{2}{\Pi r}\sum ^{r}_{j}\sqrt{2\left( (1-\sum _{i}^{m_{j}}\sqrt{x_{ij}y_{ij}}\right) }\end{displaymath}">|;
+
+$key = q/(tilde{p}_{lu}=sum^{r}_{i=1}frac{n_{i}tilde{p}_{ilu}}{rbar{n}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="126" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img28.png"
+ ALT="\( \tilde{p}_{lu}=\sum ^{r}_{i=1}\frac{n_{i}\tilde{p}_{ilu}}{r\bar{n}} \)">|;
+
+$key = q/(x_{ij});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="24" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img5.png"
+ ALT="\( x_{ij} \)">|;
+
+$key = q/{displaymath}Dr=frac{1}{r}sum^{r}_{j}sqrt{frac{sum^{m}_{i}left(x_{ij}-y_{ij}right)^{2}}{2}}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="212" HEIGHT="63" BORDER="0"
+ SRC="|."$dir".q|img18.png"
+ ALT="\begin{displaymath}
+Dr=\frac{1}{r}\sum ^{r}_{j}\sqrt{\frac{\sum ^{m}_{i}\left( x_{ij}-y_{ij}\right) ^{2}}{2}}\end{displaymath}">|;
+
+$key = q/{displaymath}a_{l}=frac{left[2sum^{r}_{i=1}n_{i}sum^{v_{l}}_{u=1}left(tilde{p}_{t)^{2}-left(r-1right)b_{l}right]}{2left(r-1right)n_{c}}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="330" HEIGHT="56" BORDER="0"
+ SRC="|."$dir".q|img34.png"
+ ALT="\begin{displaymath}
+a_{l}=\frac{\left[ 2\sum ^{r}_{i=1}n_{i}\sum ^{v_{l}}_{u=1}\...
+...^{2}-\left( r-1\right) b_{l}\right] }{2\left( r-1\right) n_{c}}\end{displaymath}">|;
+
+$key = q/(z=sum^{m}_{l=1}a_{l}^{2});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="90" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img39.png"
+ ALT="\( z=\sum ^{m}_{l=1}a_{l}^{2} \)">|;
+
+$key = q/(tilde{theta}_{L});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="21" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img42.png"
+ ALT="\( \tilde{\theta }_{L} \)">|;
+
+$key = q/(C_{XY});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="38" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img63.png"
+ ALT="\( C_{XY} \)">|;
+
+$key = q/{displaymath}Dm=frac{left(J_{X}+J_{Y}right)}{2}-J_{XY}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="175" HEIGHT="40" BORDER="0"
+ SRC="|."$dir".q|img15.png"
+ ALT="\begin{displaymath}
+Dm=\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}\end{displaymath}">|;
+
+$key = q/{displaymath}D_{R}=-logleft(frac{C_{XY}}{V_{XY}}right){displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="141" HEIGHT="45" BORDER="0"
+ SRC="|."$dir".q|img57.png"
+ ALT="\begin{displaymath}
+D_{R}=-\log \left( \frac{C_{XY}}{V_{XY}}\right) \end{displaymath}">|;
+
+$key = q/{displaymath}tilde{theta}_{L}=frac{2x+y-zpmsqrt{left(z-yright)^{2}+4x^{2}}}{2left(y-zright)}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="248" HEIGHT="57" BORDER="0"
+ SRC="|."$dir".q|img38.png"
+ ALT="\begin{displaymath}
+\tilde{\theta }_{L}=\frac{2x+y-z\pm \sqrt{\left( z-y\right) ^{2}+4x^{2}}}{2\left( y-z\right) }\end{displaymath}">|;
+
+$key = q/(W_{Y}=frac{sum^{r}_{k}sum_{ineqj}left(left|i-jright|y_{ik}y_{jk}right)}{r});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="190" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img51.png"
+ ALT="\( W_{Y}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert y_{ik}y_{jk}\right) }{r} \)">|;
+
+$key = q/(J_{Y}=frac{sum^{r}_{j}sum^{m_{j}}_{i}y^{2}_{ij}}{r});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="127" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img3.png"
+ ALT="\( J_{Y}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}y^{2}_{ij}}{r} \)">|;
+
+$key = q/{displaymath}D_{A}=1-frac{1}{r}sum^{r}_{j}sum^{m_{j}}_{i}sqrt{x_{ij}y_{ij}}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="191" HEIGHT="57" BORDER="0"
+ SRC="|."$dir".q|img22.png"
+ ALT="\begin{displaymath}
+D_{A}=1-\frac{1}{r}\sum ^{r}_{j}\sum ^{m_{j}}_{i}\sqrt{x_{ij}y_{ij}}\end{displaymath}">|;
+
+$key = q/(overline{P}_{SA_{X}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="46" HEIGHT="35" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img12.png"
+ ALT="\( \overline{P}_{SA_{X}} \)">|;
+
+$key = q/(mu_{Y_{j}}=sum_{i}iy_{ij});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="98" HEIGHT="31" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img45.png"
+ ALT="\( \mu _{Y_{j}}=\sum _{i}iy_{ij} \)">|;
+
+$key = q/{displaymath}b_{l}=2sum^{r}_{i=1}frac{n_{i}tilde{alpha}_{il}}{r(2bar{n}-1)}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="136" HEIGHT="53" BORDER="0"
+ SRC="|."$dir".q|img33.png"
+ ALT="\begin{displaymath}
+b_{l}=2\sum ^{r}_{i=1}\frac{n_{i}\tilde{\alpha }_{il}}{r(2\bar{n}-1)}\end{displaymath}">|;
+
+$key = q/(overline{mu_{X}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="26" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img53.png"
+ ALT="\( \overline{\mu _{X}} \)">|;
+
+$key = q/(J_{X}=frac{sum^{r}_{j}sum^{m_{j}}_{i}x^{2}_{ij}}{r});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="128" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img2.png"
+ ALT="\( J_{X}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x^{2}_{ij}}{r} \)">|;
+
+$key = q/(W_{X}=frac{sum^{r}_{k}sum_{ineqj}left(left|i-jright|x_{ik}x_{jk}right)}{r});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="193" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img50.png"
+ ALT="\( W_{X}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}x_{jk}\right) }{r} \)">|;
+
+$key = q/(mu_{Y_{j}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="28" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img56.png"
+ ALT="\( \mu _{Y_{j}} \)">|;
+
+$key = q/{displaymath}ASD=frac{sum^{r}_{k}sum_{i,j}left(left(i-jright)^{2}x_{ik}y_{jk}right)}{r}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="238" HEIGHT="52" BORDER="0"
+ SRC="|."$dir".q|img48.png"
+ ALT="\begin{displaymath}
+ASD=\frac{\sum ^{r}_{k}\sum _{i,j}\left( \left( i-j\right) ^{2}x_{ik}y_{jk}\right) }{r}\end{displaymath}">|;
+
+$key = q/{displaymath}Fst=frac{frac{left(J_{X}+J_{Y}right)}{2}-J_{XY}}{1-J_{XY}}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="156" HEIGHT="48" BORDER="0"
+ SRC="|."$dir".q|img17.png"
+ ALT="\begin{displaymath}
+Fst=\frac{\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}}{1-J_{XY}}\end{displaymath}">|;
+
+$key = q/(theta);MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img1.png"
+ ALT="\( \theta \)">|;
+
+$key = q/(y=sum^{m}_{l=1}b_{l}^{2});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="88" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img41.png"
+ ALT="\( y=\sum ^{m}_{l=1}b_{l}^{2} \)">|;
+
+$key = q/{displaymath}Cp=frac{sum^{r}_{j}sum^{m_{j}}_{i}left|x_{ij}-y_{ij}right|}{2r}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="176" HEIGHT="44" BORDER="0"
+ SRC="|."$dir".q|img19.png"
+ ALT="\begin{displaymath}
+Cp=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}\left\vert x_{ij}-y_{ij}\right\vert }{2r}\end{displaymath}">|;
+
+$key = q/(W_{XY}=frac{sum^{r}_{k}sum_{ineqj}left(left|i-jright|x_{ik}y_{jk}right)}{r});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="202" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img52.png"
+ ALT="\( W_{XY}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}y_{jk}\right) }{r} \)">|;
+
+$key = q/(mu_{X_{j}}=sum_{i}ix_{ij});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="103" HEIGHT="31" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img44.png"
+ ALT="\( \mu _{X_{j}}=\sum _{i}ix_{ij} \)">|;
+
+$key = q/(phi);MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="14" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img16.png"
+ ALT="\( \phi \protect \)">|;
+
+$key = q/{displaymath}D_{SW}=W_{XY}-frac{left(W_{X}+W_{Y}right)}{2}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="201" HEIGHT="40" BORDER="0"
+ SRC="|."$dir".q|img49.png"
+ ALT="\begin{displaymath}
+D_{SW}=W_{XY}-\frac{\left( W_{X}+W_{Y}\right) }{2}\end{displaymath}">|;
+
+$key = q/(C_{XY}=frac{1}{r-1}left(sum^{r}_{j}mu_{X_{j}}mu_{Y_{j}}-roverline{mu_{X}}overline{mu_{Y}}right));MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="253" HEIGHT="44" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img58.png"
+ ALT="\( C_{XY}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}\mu _{Y_{j}}-r\overline{\mu _{X}}\overline{\mu _{Y}}\right) \)">|;
+
+$key = q/(overline{P}_{SA_{Y}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="45" HEIGHT="35" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img13.png"
+ ALT="\( \overline{P}_{SA_{Y}} \)">|;
+
+$key = q/(mu_{X_{j}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="31" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img55.png"
+ ALT="\( \mu _{X_{j}} \)">|;
+
+$key = q/(C_{XY}<1);MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="67" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img62.png"
+ ALT="\( C_{XY}<1 \)">|;
+
+$key = q/(overline{mu_{Y}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="25" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img54.png"
+ ALT="\( \overline{\mu _{Y}} \)">|;
+
+$key = q/(P_{SA_{I}}=frac{sum^{r}_{j}S}{2r});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="98" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img9.png"
+ ALT="\( P_{SA_{I}}=\frac{\sum ^{r}_{j}S}{2r} \)">|;
+
+$key = q/{displaymath}left(deltamuright)^{2}=frac{sum^{r}_{j}left(mu_{X_{j}}-mu_{Y_{j}}right)^{2}}{r}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="178" HEIGHT="47" BORDER="0"
+ SRC="|."$dir".q|img47.png"
+ ALT="\begin{displaymath}
+\left( \delta \mu \right) ^{2}=\frac{\sum ^{r}_{j}\left( \mu _{X_{j}}-\mu _{Y_{j}}\right) ^{2}}{r}\end{displaymath}">|;
+
+$key = q/(D_{SA_{I}}=1-P_{SA_{I}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="127" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img8.png"
+ ALT="\( D_{SA_{I}}=1-P_{SA_{I}} \)">|;
+
+$key = q/{displaymath}tilde{theta}_{U}=frac{1}{m}sum^{m}_{l=1}tilde{theta}_{l}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="97" HEIGHT="54" BORDER="0"
+ SRC="|."$dir".q|img31.png"
+ ALT="\begin{displaymath}
+\tilde{\theta }_{U}=\frac{1}{m}\sum ^{m}_{l=1}\tilde{\theta }_{l}\end{displaymath}">|;
+
+$key = q/(tilde{alpha}_{il}=1-sum^{v_{l}}_{u=1}tilde{p}_{ilu}^{2});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="141" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img29.png"
+ ALT="\( \tilde{\alpha }_{il}=1-\sum ^{v_{l}}_{u=1}\tilde{p}_{ilu}^{2} \)">|;
+
+$key = q/(x=sum^{m}_{l=1}a_{l}b_{l});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="100" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img40.png"
+ ALT="\( x=\sum ^{m}_{l=1}a_{l}b_{l} \)">|;
+
+$key = q/(D_{A});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="28" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img21.png"
+ ALT="\( D_{A}\protect \)">|;
+
+$key = q/(V_{X}=frac{1}{r-1}left(sum^{r}_{j}mu_{X_{j}}^{2}-roverline{mu_{X}}^{2}right));MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="204" HEIGHT="44" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img60.png"
+ ALT="\( V_{X}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}^{2}-r\overline{\mu _{X}}^{2}\right) \)">|;
+
+$key = q/(V_{Y}=frac{1}{r-1}left(sum^{r}_{j}mu_{Y_{j}}^{2}-roverline{mu_{Y}}^{2}right));MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="199" HEIGHT="44" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img61.png"
+ ALT="\( V_{Y}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{Y_{j}}^{2}-r\overline{\mu _{Y}}^{2}\right) \)">|;
+
+$key = q/(i);MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="10" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="|."$dir".q|img46.png"
+ ALT="\( i \)">|;
+
+$key = q/(V_{XY}=frac{1}{2}left(V_{X}+V_{Y}right));MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="143" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img59.png"
+ ALT="\( V_{XY}=\frac{1}{2}\left( V_{X}+V_{Y}\right) \)">|;
+
+$key = q/(tilde{theta}_{U});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="22" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img30.png"
+ ALT="\( \tilde{\theta }_{U}\protect \)">|;
+
+$key = q/(J_{XY}=frac{sum^{r}_{j}sum^{m_{j}}_{i}x_{ij}y_{ij}}{r});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="155" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img4.png"
+ ALT="\( J_{XY}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x_{ij}y_{ij}}{r} \)">|;
+
+$key = q/(overline{P}_{SA_{B}});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="45" HEIGHT="35" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img11.png"
+ ALT="\( \overline{P}_{SA_{B}} \)">|;
+
+$key = q/{displaymath}D_{SA_{B}}=1-frac{2overline{P}_{SA_{B}}}{overline{P}_{SA_{X}}+overline{P}_{SA_{Y}}}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="194" HEIGHT="48" BORDER="0"
+ SRC="|."$dir".q|img10.png"
+ ALT="\begin{displaymath}
+D_{SA_{B}}=1-\frac{2\overline{P}_{SA_{B}}}{\overline{P}_{SA_{X}}+\overline{P}_{SA_{Y}}}\end{displaymath}">|;
+
+$key = q/(m_{j});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="25" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img7.png"
+ ALT="\( m_{j} \)">|;
+
+$key = q/{displaymath}a_{l}+b_{l}=frac{1}{2}sum_{u}left(tilde{p}_{1lu}-tilde{p}_{2lu}righalpha}_{2l}right)}{4n_{1}n_{2}left(n_{1}+n_{2}-1right)}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="456" HEIGHT="49" BORDER="0"
+ SRC="|."$dir".q|img36.png"
+ ALT="\begin{displaymath}
+a_{l}+b_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tild...
+...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}">|;
+
+$key = q/(bar{n}=sum^{r}_{i=1}frac{n_{i}}{r});MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="92" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="|."$dir".q|img26.png"
+ ALT="\( \bar{n}=\sum ^{r}_{i=1}\frac{n_{i}}{r} \)">|;
+
+$key = q/{displaymath}tilde{theta}_{W}=frac{left(sum^{m}_{l=1}a_{l}right)}{sum^{m}_{l=1}left(a_{l}+b_{l}right)}{displaymath};MSF=1.6;AAT/;
+$cached_env_img{$key} = q|<IMG
+ WIDTH="143" HEIGHT="46" BORDER="0"
+ SRC="|."$dir".q|img37.png"
+ ALT="\begin{displaymath}
+\tilde{\theta }_{W}=\frac{\left( \sum ^{m}_{l=1}a_{l}\right) }{\sum ^{m}_{l=1}\left( a_{l}+b_{l}\right) }\end{displaymath}">|;
+
+1;
+
diff --git a/html/old_formula/images.tex b/html/old_formula/images.tex
new file mode 100755
index 0000000..b7475ba
--- /dev/null
+++ b/html/old_formula/images.tex
@@ -0,0 +1,543 @@
+\batchmode
+
+\documentclass[english]{report}
+\RequirePackage{ifthen}
+
+
+\usepackage[T1]{fontenc}
+\usepackage[latin1]{inputenc}
+\usepackage{babel}
+\setlength\parskip{\medskipamount}
+\setlength\parindent{0pt}
+
+\makeatletter
+
+%
+\providecommand{\LyX}{L\kern-.1667em\lower.25em\hbox{Y}\kern-.125emX\@}
+\makeatother
+
+\usepackage[dvips]{color}
+
+
+\pagecolor[gray]{.7}
+
+\usepackage[]{inputenc}
+
+
+
+\makeatletter
+
+\makeatletter
+\count@=\the\catcode`\_ \catcode`\_=8
+\newenvironment{tex2html_wrap}{}{}%
+\catcode`\<=12\catcode`\_=\count@
+\newcommand{\providedcommand}[1]{\expandafter\providecommand\csname #1\endcsname}%
+\newcommand{\renewedcommand}[1]{\expandafter\providecommand\csname #1\endcsname{}%
+ \expandafter\renewcommand\csname #1\endcsname}%
+\newcommand{\newedenvironment}[1]{\newenvironment{#1}{}{}\renewenvironment{#1}}%
+\let\newedcommand\renewedcommand
+\let\renewedenvironment\newedenvironment
+\makeatother
+\let\mathon=$
+\let\mathoff=$
+\ifx\AtBeginDocument\undefined \newcommand{\AtBeginDocument}[1]{}\fi
+\newbox\sizebox
+\setlength{\hoffset}{0pt}\setlength{\voffset}{0pt}
+\addtolength{\textheight}{\footskip}\setlength{\footskip}{0pt}
+\addtolength{\textheight}{\topmargin}\setlength{\topmargin}{0pt}
+\addtolength{\textheight}{\headheight}\setlength{\headheight}{0pt}
+\addtolength{\textheight}{\headsep}\setlength{\headsep}{0pt}
+\setlength{\textwidth}{349pt}
+\newwrite\lthtmlwrite
+\makeatletter
+\let\realnormalsize=\normalsize
+\global\topskip=2sp
+\def\preveqno{}\let\real at float=\@float \let\realend at float=\end at float
+\def\@float{\let\@savefreelist\@freelist\real at float}
+\def\liih at math{\ifmmode$\else\bad at math\fi}
+\def\end at float{\realend at float\global\let\@freelist\@savefreelist}
+\let\real at dbflt=\@dbflt \let\end at dblfloat=\end at float
+\let\@largefloatcheck=\relax
+\let\if at boxedmulticols=\iftrue
+\def\@dbflt{\let\@savefreelist\@freelist\real at dbflt}
+\def\adjustnormalsize{\def\normalsize{\mathsurround=0pt \realnormalsize
+ \parindent=0pt\abovedisplayskip=0pt\belowdisplayskip=0pt}%
+ \def\phantompar{\csname par\endcsname}\normalsize}%
+\def\lthtmltypeout#1{{\let\protect\string \immediate\write\lthtmlwrite{#1}}}%
+\newcommand\lthtmlhboxmathA{\adjustnormalsize\setbox\sizebox=\hbox\bgroup\kern.05em }%
+\newcommand\lthtmlhboxmathB{\adjustnormalsize\setbox\sizebox=\hbox to\hsize\bgroup\hfill }%
+\newcommand\lthtmlvboxmathA{\adjustnormalsize\setbox\sizebox=\vbox\bgroup %
+ \let\ifinner=\iffalse \let\)\liih at math }%
+\newcommand\lthtmlboxmathZ{\@next\next\@currlist{}{\def\next{\voidb at x}}%
+ \expandafter\box\next\egroup}%
+\newcommand\lthtmlmathtype[1]{\gdef\lthtmlmathenv{#1}}%
+\newcommand\lthtmllogmath{\lthtmltypeout{l2hSize %
+:\lthtmlmathenv:\the\ht\sizebox::\the\dp\sizebox::\the\wd\sizebox.\preveqno}}%
+\newcommand\lthtmlfigureA[1]{\let\@savefreelist\@freelist
+ \lthtmlmathtype{#1}\lthtmlvboxmathA}%
+\newcommand\lthtmlpictureA{\bgroup\catcode`\_=8 \lthtmlpictureB}%
+\newcommand\lthtmlpictureB[1]{\lthtmlmathtype{#1}\egroup
+ \let\@savefreelist\@freelist \lthtmlhboxmathB}%
+\newcommand\lthtmlpictureZ[1]{\hfill\lthtmlfigureZ}%
+\newcommand\lthtmlfigureZ{\lthtmlboxmathZ\lthtmllogmath\copy\sizebox
+ \global\let\@freelist\@savefreelist}%
+\newcommand\lthtmldisplayA{\bgroup\catcode`\_=8 \lthtmldisplayAi}%
+\newcommand\lthtmldisplayAi[1]{\lthtmlmathtype{#1}\egroup\lthtmlvboxmathA}%
+\newcommand\lthtmldisplayB[1]{\edef\preveqno{(\theequation)}%
+ \lthtmldisplayA{#1}\let\@eqnnum\relax}%
+\newcommand\lthtmldisplayZ{\lthtmlboxmathZ\lthtmllogmath\lthtmlsetmath}%
+\newcommand\lthtmlinlinemathA{\bgroup\catcode`\_=8 \lthtmlinlinemathB}
+\newcommand\lthtmlinlinemathB[1]{\lthtmlmathtype{#1}\egroup\lthtmlhboxmathA
+ \vrule height1.5ex width0pt }%
+\newcommand\lthtmlinlineA{\bgroup\catcode`\_=8 \lthtmlinlineB}%
+\newcommand\lthtmlinlineB[1]{\lthtmlmathtype{#1}\egroup\lthtmlhboxmathA}%
+\newcommand\lthtmlinlineZ{\egroup\expandafter\ifdim\dp\sizebox>0pt %
+ \expandafter\centerinlinemath\fi\lthtmllogmath\lthtmlsetinline}
+\newcommand\lthtmlinlinemathZ{\egroup\expandafter\ifdim\dp\sizebox>0pt %
+ \expandafter\centerinlinemath\fi\lthtmllogmath\lthtmlsetmath}
+\newcommand\lthtmlindisplaymathZ{\egroup %
+ \centerinlinemath\lthtmllogmath\lthtmlsetmath}
+\def\lthtmlsetinline{\hbox{\vrule width.1em \vtop{\vbox{%
+ \kern.1em\copy\sizebox}\ifdim\dp\sizebox>0pt\kern.1em\else\kern.3pt\fi
+ \ifdim\hsize>\wd\sizebox \hrule depth1pt\fi}}}
+\def\lthtmlsetmath{\hbox{\vrule width.1em\kern-.05em\vtop{\vbox{%
+ \kern.1em\kern0.8 pt\hbox{\hglue.17em\copy\sizebox\hglue0.8 pt}}\kern.3pt%
+ \ifdim\dp\sizebox>0pt\kern.1em\fi \kern0.8 pt%
+ \ifdim\hsize>\wd\sizebox \hrule depth1pt\fi}}}
+\def\centerinlinemath{%
+ \dimen1=\ifdim\ht\sizebox<\dp\sizebox \dp\sizebox\else\ht\sizebox\fi
+ \advance\dimen1by.5pt \vrule width0pt height\dimen1 depth\dimen1
+ \dp\sizebox=\dimen1\ht\sizebox=\dimen1\relax}
+
+\def\lthtmlcheckvsize{\ifdim\ht\sizebox<\vsize
+ \ifdim\wd\sizebox<\hsize\expandafter\hfill\fi \expandafter\vfill
+ \else\expandafter\vss\fi}%
+\providecommand{\selectlanguage}[1]{}%
+\makeatletter \tracingstats = 1
+
+
+\begin{document}
+\pagestyle{empty}\thispagestyle{empty}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength hsize=\the\hsize}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength vsize=\the\vsize}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength hoffset=\the\hoffset}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength voffset=\the\voffset}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength topmargin=\the\topmargin}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength topskip=\the\topskip}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength headheight=\the\headheight}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength headsep=\the\headsep}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength parskip=\the\parskip}\lthtmltypeout{}%
+\lthtmltypeout{latex2htmlLength oddsidemargin=\the\oddsidemargin}\lthtmltypeout{}%
+\makeatletter
+\if at twoside\lthtmltypeout{latex2htmlLength evensidemargin=\the\evensidemargin}%
+\else\lthtmltypeout{latex2htmlLength evensidemargin=\the\oddsidemargin}\fi%
+\lthtmltypeout{}%
+\makeatother
+\setcounter{page}{1}
+\onecolumn
+
+% !!! IMAGES START HERE !!!
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline797}%
+\( \theta \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline481}%
+\( J_{X}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x^{2}_{ij}}{r} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline482}%
+\( J_{Y}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}y^{2}_{ij}}{r} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline483}%
+\( J_{XY}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x_{ij}y_{ij}}{r} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline484}%
+\( x_{ij} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline485}%
+\( y_{ij} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline486}%
+\( m_{j} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline487}%
+\( D_{SA_{I}}=1-P_{SA_{I}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline488}%
+\( P_{SA_{I}}=\frac{\sum ^{r}_{j}S}{2r} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath569}%
+\begin{displaymath}
+D_{SA_{B}}=1-\frac{2\overline{P}_{SA_{B}}}{\overline{P}_{SA_{X}}+\overline{P}_{SA_{Y}}}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline489}%
+\( \overline{P}_{SA_{B}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline490}%
+\( \overline{P}_{SA_{X}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline491}%
+\( \overline{P}_{SA_{Y}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath570}%
+\begin{displaymath}
+Ds=-\ln \left[ \frac{J_{XY}}{\sqrt{J_{X}J_{Y}}}\right] \end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath571}%
+\begin{displaymath}
+Dm=\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline492}%
+\( \phi \protect \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath572}%
+\begin{displaymath}
+Fst=\frac{\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}}{1-J_{XY}}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath573}%
+\begin{displaymath}
+Dr=\frac{1}{r}\sum ^{r}_{j}\sqrt{\frac{\sum ^{m}_{i}\left( x_{ij}-y_{ij}\right) ^{2}}{2}}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath574}%
+\begin{displaymath}
+Cp=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}\left| x_{ij}-y_{ij}\right| }{2r}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath575}%
+\begin{displaymath}
+Dc=\frac{2}{\Pi r}\sum ^{r}_{j}\sqrt{2\left( (1-\sum _{i}^{m_{j}}\sqrt{x_{ij}y_{ij}}\right) }\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline493}%
+\( D_{A}\protect \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath576}%
+\begin{displaymath}
+D_{A}=1-\frac{1}{r}\sum ^{r}_{j}\sum ^{m_{j}}_{i}\sqrt{x_{ij}y_{ij}}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline494}%
+\( X^{2}\protect \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath577}%
+\begin{displaymath}
+X^{2}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}2\frac{\left( x_{ij}-y_{ij}\right) ^{2}}{\left( x_{ij}+y_{ij}\right) }}{r}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath578}%
+\begin{displaymath}
+DReynold=-\ln (1-\theta )\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline496}%
+\( \bar{n}=\sum ^{r}_{i=1}\frac{n_{i}}{r} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline497}%
+\( n_{c}=\frac{\left( r\bar{n}-\sum ^{r}_{i=1}\frac{n^{2}_{i}}{r\bar{n}}\right) }{\left( r-1\right) } \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline498}%
+\( \tilde{p}_{lu}=\sum ^{r}_{i=1}\frac{n_{i}\tilde{p}_{ilu}}{r\bar{n}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline499}%
+\( \tilde{\alpha }_{il}=1-\sum ^{v_{l}}_{u=1}\tilde{p}_{ilu}^{2} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline500}%
+\( \tilde{\theta }_{U}\protect \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath579}%
+\begin{displaymath}
+\tilde{\theta }_{U}=\frac{1}{m}\sum ^{m}_{l=1}\tilde{\theta }_{l}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline501}%
+\( \tilde{\theta }_{l}=\frac{a_{l}}{a_{l}+b_{l}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath580}%
+\begin{displaymath}
+b_{l}=2\sum ^{r}_{i=1}\frac{n_{i}\tilde{\alpha }_{il}}{r(2\bar{n}-1)}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath581}%
+\begin{displaymath}
+a_{l}=\frac{\left[ 2\sum ^{r}_{i=1}n_{i}\sum ^{v_{l}}_{u=1}\left( \tilde{p}_{ilu}-\tilde{p}_{lu}\right) ^{2}-\left( r-1\right) b_{l}\right] }{2\left( r-1\right) n_{c}}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath582}%
+\begin{displaymath}
+a_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{2lu}\right) ^{2}-\frac{\left( n_{1}+n_{2}\right) \left( n_{1}\tilde{\alpha }_{1l}+n_{2}\tilde{\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath583}%
+\begin{displaymath}
+a_{l}+b_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{2lu}\right) ^{2}+\frac{\left( 4n_{1}n_{2}-n_{1}-n_{2}\right) \left( n_{1}\tilde{\alpha }_{1l}+n_{2}\tilde{\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath584}%
+\begin{displaymath}
+\tilde{\theta }_{W}=\frac{\left( \sum ^{m}_{l=1}a_{l}\right) }{\sum ^{m}_{l=1}\left( a_{l}+b_{l}\right) }\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+\stepcounter{subsubsection}
+{\newpage\clearpage
+\lthtmldisplayA{displaymath585}%
+\begin{displaymath}
+\tilde{\theta }_{L}=\frac{2x+y-z\pm \sqrt{\left( z-y\right) ^{2}+4x^{2}}}{2\left( y-z\right) }\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline503}%
+\( z=\sum ^{m}_{l=1}a_{l}^{2} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline504}%
+\( x=\sum ^{m}_{l=1}a_{l}b_{l} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline505}%
+\( y=\sum ^{m}_{l=1}b_{l}^{2} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline506}%
+\( \tilde{\theta }_{L} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath586}%
+\begin{displaymath}
+R=\frac{\left( 2x+y+z\right) \tilde{\theta }_{L}^{2}-2\left( x+z\right) \tilde{\theta }_{L}+z}{1-2\tilde{\theta }_{L}+2\tilde{\theta }_{L}^{2}}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline507}%
+\( \mu _{X_{j}}=\sum _{i}ix_{ij} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline508}%
+\( \mu _{Y_{j}}=\sum _{i}iy_{ij} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline511}%
+\( i \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath587}%
+\begin{displaymath}
+\left( \delta \mu \right) ^{2}=\frac{\sum ^{r}_{j}\left( \mu _{X_{j}}-\mu _{Y_{j}}\right) ^{2}}{r}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath588}%
+\begin{displaymath}
+ASD=\frac{\sum ^{r}_{k}\sum _{i,j}\left( \left( i-j\right) ^{2}x_{ik}y_{jk}\right) }{r}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath589}%
+\begin{displaymath}
+D_{SW}=W_{XY}-\frac{\left( W_{X}+W_{Y}\right) }{2}\end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline512}%
+\( W_{X}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left| i-j\right| x_{ik}x_{jk}\right) }{r} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline513}%
+\( W_{Y}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left| i-j\right| y_{ik}y_{jk}\right) }{r} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline514}%
+\( W_{XY}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left| i-j\right| x_{ik}y_{jk}\right) }{r} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline515}%
+\( \overline{\mu _{X}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline516}%
+\( \overline{\mu _{Y}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline517}%
+\( \mu _{X_{j}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline518}%
+\( \mu _{Y_{j}} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmldisplayA{displaymath590}%
+\begin{displaymath}
+D_{R}=-\log \left( \frac{C_{XY}}{V_{XY}}\right) \end{displaymath}%
+\lthtmldisplayZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline519}%
+\( C_{XY}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}\mu _{Y_{j}}-r\overline{\mu _{X}}\overline{\mu _{Y}}\right) \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline520}%
+\( V_{XY}=\frac{1}{2}\left( V_{X}+V_{Y}\right) \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline521}%
+\( V_{X}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}^{2}-r\overline{\mu _{X}}^{2}\right) \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline522}%
+\( V_{Y}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{Y_{j}}^{2}-r\overline{\mu _{Y}}^{2}\right) \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline523}%
+\( C_{XY}<1 \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+{\newpage\clearpage
+\lthtmlinlinemathA{tex2html_wrap_inline524}%
+\( C_{XY} \)%
+\lthtmlinlinemathZ
+\lthtmlcheckvsize\clearpage}
+
+
+\end{document}
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diff --git a/html/old_formula/index.html b/html/old_formula/index.html
new file mode 100755
index 0000000..7947cf5
--- /dev/null
+++ b/html/old_formula/index.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>formules</TITLE>
+<META NAME="description" CONTENT="formules">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node1.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html2"
+ HREF="node1.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up_g.png">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev_g.png">
+<BR>
+<B> Next:</B> <A NAME="tex2html3"
+ HREF="node1.html">Distances</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"></A>
+
+<UL>
+<LI><A NAME="tex2html4"
+ HREF="node1.html">Distances</A>
+<UL>
+<LI><A NAME="tex2html5"
+ HREF="node2.html">IAM distances</A>
+<UL>
+<LI><A NAME="tex2html6"
+ HREF="node3.html">Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]</A>
+<LI><A NAME="tex2html7"
+ HREF="node4.html">Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html8"
+ HREF="node5.html">Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html9"
+ HREF="node6.html">Latter's (1972) Fst (=<IMG
+ WIDTH="14" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img16.png"
+ ALT="\( \phi \protect \)">*) distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html10"
+ HREF="node7.html">Rogers' (1972) distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html11"
+ HREF="node8.html">Prevosti et al's (1975) distance [Takezaki, N. 96] has a statistical property
+similar to that of Dr and is defined as</A>
+<LI><A NAME="tex2html12"
+ HREF="node9.html">Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html13"
+ HREF="node10.html">Nei et al's (1983) <IMG
+ WIDTH="28" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img21.png"
+ ALT="\( D_{A}\protect \)"> distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html14"
+ HREF="node11.html">Sanghvi's (1953) <IMG
+ WIDTH="26" HEIGHT="16" ALIGN="BOTTOM" BORDER="0"
+ SRC="img23.png"
+ ALT="\( X^{2}\protect \)"> distance[Takezaki, N. 96]</A>
+<LI><A NAME="tex2html15"
+ HREF="node12.html">Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]</A>
+<UL>
+<LI><A NAME="tex2html16"
+ HREF="node13.html">unweighted average of single-locus ratio estimators, <!-- MATH
+ $\tilde{\theta }_{U}\protect$
+ -->
+<IMG
+ WIDTH="22" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img30.png"
+ ALT="\( \tilde{\theta }_{U}\protect \)">:</A>
+<LI><A NAME="tex2html17"
+ HREF="node14.html">weighted average of single-locus ratio estimators :</A>
+<LI><A NAME="tex2html18"
+ HREF="node15.html">least squares <!-- MATH
+ $\theta \protect$
+ -->
+<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="\( \theta \)"> estimator :</A>
+</UL>
+</UL>
+<LI><A NAME="tex2html19"
+ HREF="node16.html">SMM distances</A>
+<UL>
+<LI><A NAME="tex2html20"
+ HREF="node17.html">Goldstein et al. (1995a) [Goldstein, D.B. 97]</A>
+<LI><A NAME="tex2html21"
+ HREF="node18.html">average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995)
+[Goldstein, D.B. 97]</A>
+<LI><A NAME="tex2html22"
+ HREF="node19.html">Shriver et al.'s (1995) [Shriver, M.D. 95]</A>
+<LI><A NAME="tex2html23"
+ HREF="node20.html">Lev A. Zhivotovsky (1999) [Takezaki, N. 96]</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html24"
+ HREF="node21.html">Bibliography</A>
+<LI><A NAME="tex2html25"
+ HREF="node22.html">About this document ...</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/internals.pl b/html/old_formula/internals.pl
new file mode 100755
index 0000000..ba73fb5
--- /dev/null
+++ b/html/old_formula/internals.pl
@@ -0,0 +1,26 @@
+# LaTeX2HTML 2K.1beta (1.48)
+# Associate internals original text with physical files.
+
+
+$key = q/cite_RWC83/;
+$ref_files{$key} = "$dir".q|node21.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_SJB95/;
+$ref_files{$key} = "$dir".q|node21.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_TN96/;
+$ref_files{$key} = "$dir".q|node21.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_GP97/;
+$ref_files{$key} = "$dir".q|node21.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_JC93/;
+$ref_files{$key} = "$dir".q|node21.html|;
+$noresave{$key} = "$nosave";
+
+1;
+
diff --git a/html/old_formula/labels.pl b/html/old_formula/labels.pl
new file mode 100755
index 0000000..22af47f
--- /dev/null
+++ b/html/old_formula/labels.pl
@@ -0,0 +1,33 @@
+# LaTeX2HTML 2K.1beta (1.48)
+# Associate labels original text with physical files.
+
+
+$key = q/cite_RWC83/;
+$external_labels{$key} = "$URL/" . q|node21.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_SJB95/;
+$external_labels{$key} = "$URL/" . q|node21.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_TN96/;
+$external_labels{$key} = "$URL/" . q|node21.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_GP97/;
+$external_labels{$key} = "$URL/" . q|node21.html|;
+$noresave{$key} = "$nosave";
+
+$key = q/cite_JC93/;
+$external_labels{$key} = "$URL/" . q|node21.html|;
+$noresave{$key} = "$nosave";
+
+1;
+
+
+# LaTeX2HTML 2K.1beta (1.48)
+# labels from external_latex_labels array.
+
+
+1;
+
diff --git a/html/old_formula/next_motif.gif b/html/old_formula/next_motif.gif
new file mode 100755
index 0000000..7a2dbe9
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diff --git a/html/old_formula/next_motif_gr.gif b/html/old_formula/next_motif_gr.gif
new file mode 100755
index 0000000..1416b1c
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diff --git a/html/old_formula/node1.html b/html/old_formula/node1.html
new file mode 100755
index 0000000..7a5bf04
--- /dev/null
+++ b/html/old_formula/node1.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Distances</TITLE>
+<META NAME="description" CONTENT="Distances">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node21.html">
+<LINK REL="previous" HREF="formules.html">
+<LINK REL="up" HREF="formules.html">
+<LINK REL="next" HREF="node2.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html34"
+ HREF="node2.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html32"
+ HREF="formules.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html26"
+ HREF="formules.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html35"
+ HREF="node2.html">IAM distances</A>
+<B> Up:</B> <A NAME="tex2html33"
+ HREF="formules.html">formules</A>
+<B> Previous:</B> <A NAME="tex2html27"
+ HREF="formules.html">formules</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00100000000000000000">
+Distances</A>
+</H1>
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html36"
+ HREF="node2.html">IAM distances</A>
+<UL>
+<LI><A NAME="tex2html37"
+ HREF="node3.html">Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]</A>
+<LI><A NAME="tex2html38"
+ HREF="node4.html">Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html39"
+ HREF="node5.html">Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html40"
+ HREF="node6.html">Latter's (1972) Fst (=<IMG
+ WIDTH="14" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img16.png"
+ ALT="\( \phi \protect \)">*) distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html41"
+ HREF="node7.html">Rogers' (1972) distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html42"
+ HREF="node8.html">Prevosti et al's (1975) distance [Takezaki, N. 96] has a statistical property
+similar to that of Dr and is defined as</A>
+<LI><A NAME="tex2html43"
+ HREF="node9.html">Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html44"
+ HREF="node10.html">Nei et al's (1983) <IMG
+ WIDTH="28" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img21.png"
+ ALT="\( D_{A}\protect \)"> distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html45"
+ HREF="node11.html">Sanghvi's (1953) <IMG
+ WIDTH="26" HEIGHT="16" ALIGN="BOTTOM" BORDER="0"
+ SRC="img23.png"
+ ALT="\( X^{2}\protect \)"> distance[Takezaki, N. 96]</A>
+<LI><A NAME="tex2html46"
+ HREF="node12.html">Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]</A>
+<UL>
+<LI><A NAME="tex2html47"
+ HREF="node13.html">unweighted average of single-locus ratio estimators, <!-- MATH
+ $\tilde{\theta }_{U}\protect$
+ -->
+<IMG
+ WIDTH="22" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img30.png"
+ ALT="\( \tilde{\theta }_{U}\protect \)">:</A>
+<LI><A NAME="tex2html48"
+ HREF="node14.html">weighted average of single-locus ratio estimators :</A>
+<LI><A NAME="tex2html49"
+ HREF="node15.html">least squares <!-- MATH
+ $\theta \protect$
+ -->
+<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="\( \theta \)"> estimator :</A>
+</UL>
+</UL>
+<BR>
+<LI><A NAME="tex2html50"
+ HREF="node16.html">SMM distances</A>
+<UL>
+<LI><A NAME="tex2html51"
+ HREF="node17.html">Goldstein et al. (1995a) [Goldstein, D.B. 97]</A>
+<LI><A NAME="tex2html52"
+ HREF="node18.html">average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995)
+[Goldstein, D.B. 97]</A>
+<LI><A NAME="tex2html53"
+ HREF="node19.html">Shriver et al.'s (1995) [Shriver, M.D. 95]</A>
+<LI><A NAME="tex2html54"
+ HREF="node20.html">Lev A. Zhivotovsky (1999) [Takezaki, N. 96]</A>
+</UL></UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node10.html b/html/old_formula/node10.html
new file mode 100755
index 0000000..66539e8
--- /dev/null
+++ b/html/old_formula/node10.html
@@ -0,0 +1,86 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Nei et al's (1983) distance [Takezaki, N. 96]</TITLE>
+<META NAME="description" CONTENT="Nei et al's (1983) distance [Takezaki, N. 96]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node11.html">
+<LINK REL="previous" HREF="node9.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node11.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html156"
+ HREF="node11.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html154"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html148"
+ HREF="node9.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html157"
+ HREF="node11.html">Sanghvi's (1953) distance[Takezaki, N. 96]</A>
+<B> Up:</B> <A NAME="tex2html155"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html149"
+ HREF="node9.html">Cavali-Sforza and Edwards' (1967)</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00118000000000000000">
+Nei et al's (1983) <IMG
+ WIDTH="28" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img21.png"
+ ALT="\( D_{A}\protect \)"> distance [<A
+ HREF="node21.html#TN96">Takezaki, N. 96</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+D_{A}=1-\frac{1}{r}\sum ^{r}_{j}\sum ^{m_{j}}_{i}\sqrt{x_{ij}y_{ij}}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="191" HEIGHT="57" BORDER="0"
+ SRC="img22.png"
+ ALT="\begin{displaymath}
+D_{A}=1-\frac{1}{r}\sum ^{r}_{j}\sum ^{m_{j}}_{i}\sqrt{x_{ij}y_{ij}}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node11.html b/html/old_formula/node11.html
new file mode 100755
index 0000000..808a907
--- /dev/null
+++ b/html/old_formula/node11.html
@@ -0,0 +1,86 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Sanghvi's (1953) distance[Takezaki, N. 96]</TITLE>
+<META NAME="description" CONTENT="Sanghvi's (1953) distance[Takezaki, N. 96]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
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+
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+<!--Navigation Panel-->
+<A NAME="tex2html166"
+ HREF="node12.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html164"
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+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
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+ HREF="node10.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html167"
+ HREF="node12.html">Reynold's genetic distance for</A>
+<B> Up:</B> <A NAME="tex2html165"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html159"
+ HREF="node10.html">Nei et al's (1983)</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00119000000000000000">
+Sanghvi's (1953) <IMG
+ WIDTH="26" HEIGHT="16" ALIGN="BOTTOM" BORDER="0"
+ SRC="img23.png"
+ ALT="\( X^{2}\protect \)"> distance[<A
+ HREF="node21.html#TN96">Takezaki, N. 96</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+X^{2}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}2\frac{\left( x_{ij}-y_{ij}\right) ^{2}}{\left( x_{ij}+y_{ij}\right) }}{r}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="180" HEIGHT="50" BORDER="0"
+ SRC="img24.png"
+ ALT="\begin{displaymath}
+X^{2}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}2\frac{\left( x_{ij}-y_{ij}\right) ^{2}}{\left( x_{ij}+y_{ij}\right) }}{r}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node12.html b/html/old_formula/node12.html
new file mode 100755
index 0000000..b66a14b
--- /dev/null
+++ b/html/old_formula/node12.html
@@ -0,0 +1,142 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]</TITLE>
+<META NAME="description" CONTENT="Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
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+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html175"
+ HREF="node13.html">unweighted average of single-locus</A>
+<B> Up:</B> <A NAME="tex2html173"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html169"
+ HREF="node11.html">Sanghvi's (1953) distance[Takezaki, N. 96]</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION001110000000000000000">
+Reynold's genetic distance for short-term evolution (1983) [<A
+ HREF="node21.html#RWC83">Reynolds, J. 83</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+DReynold=-\ln (1-\theta )
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="168" HEIGHT="28" BORDER="0"
+ SRC="img25.png"
+ ALT="\begin{displaymath}
+DReynold=-\ln (1-\theta )\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+the following notation is used, for all <IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="\( \theta \)"> estimators:
+
+<P>
+<!-- MATH
+ $\bar{n}=\sum ^{r}_{i=1}\frac{n_{i}}{r}$
+ -->
+<IMG
+ WIDTH="92" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="img26.png"
+ ALT="\( \bar{n}=\sum ^{r}_{i=1}\frac{n_{i}}{r} \)">, <!-- MATH
+ $n_{c}=\frac{\left( r\bar{n}-\sum ^{r}_{i=1}\frac{n^{2}_{i}}{r\bar{n}}\right) }{\left( r-1\right) }$
+ -->
+<IMG
+ WIDTH="143" HEIGHT="74" ALIGN="MIDDLE" BORDER="0"
+ SRC="img27.png"
+ ALT="\( n_{c}=\frac{\left( r\bar{n}-\sum ^{r}_{i=1}\frac{n^{2}_{i}}{r\bar{n}}\right) }{\left( r-1\right) } \)">,
+<!-- MATH
+ $\tilde{p}_{lu}=\sum ^{r}_{i=1}\frac{n_{i}\tilde{p}_{ilu}}{r\bar{n}}$
+ -->
+<IMG
+ WIDTH="126" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img28.png"
+ ALT="\( \tilde{p}_{lu}=\sum ^{r}_{i=1}\frac{n_{i}\tilde{p}_{ilu}}{r\bar{n}} \)">,
+<!-- MATH
+ $\tilde{\alpha }_{il}=1-\sum ^{v_{l}}_{u=1}\tilde{p}_{ilu}^{2}$
+ -->
+<IMG
+ WIDTH="141" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="img29.png"
+ ALT="\( \tilde{\alpha }_{il}=1-\sum ^{v_{l}}_{u=1}\tilde{p}_{ilu}^{2} \)">
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html176"
+ HREF="node13.html">unweighted average of single-locus ratio estimators, <!-- MATH
+ $\tilde{\theta }_{U}\protect$
+ -->
+<IMG
+ WIDTH="22" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img30.png"
+ ALT="\( \tilde{\theta }_{U}\protect \)">:</A>
+<LI><A NAME="tex2html177"
+ HREF="node14.html">weighted average of single-locus ratio estimators :</A>
+<LI><A NAME="tex2html178"
+ HREF="node15.html">least squares <!-- MATH
+ $\theta \protect$
+ -->
+<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="\( \theta \)"> estimator :</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node13.html b/html/old_formula/node13.html
new file mode 100755
index 0000000..8c0d722
--- /dev/null
+++ b/html/old_formula/node13.html
@@ -0,0 +1,180 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>unweighted average of single-locus ratio estimators, :</TITLE>
+<META NAME="description" CONTENT="unweighted average of single-locus ratio estimators, :">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
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+<LINK REL="previous" HREF="node12.html">
+<LINK REL="up" HREF="node12.html">
+<LINK REL="next" HREF="node14.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html187"
+ HREF="node14.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html185"
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+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
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+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html188"
+ HREF="node14.html">weighted average of single-locus</A>
+<B> Up:</B> <A NAME="tex2html186"
+ HREF="node12.html">Reynold's genetic distance for</A>
+<B> Previous:</B> <A NAME="tex2html180"
+ HREF="node12.html">Reynold's genetic distance for</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H3><A NAME="SECTION001110100000000000000">
+unweighted average of single-locus ratio estimators, <!-- MATH
+ $\tilde{\theta }_{U}\protect$
+ -->
+<IMG
+ WIDTH="22" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img30.png"
+ ALT="\( \tilde{\theta }_{U}\protect \)">:</A>
+</H3>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+\tilde{\theta }_{U}=\frac{1}{m}\sum ^{m}_{l=1}\tilde{\theta }_{l}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="97" HEIGHT="54" BORDER="0"
+ SRC="img31.png"
+ ALT="\begin{displaymath}
+\tilde{\theta }_{U}=\frac{1}{m}\sum ^{m}_{l=1}\tilde{\theta }_{l}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+, with <!-- MATH
+ $\tilde{\theta }_{l}=\frac{a_{l}}{a_{l}+b_{l}}$
+ -->
+<IMG
+ WIDTH="73" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img32.png"
+ ALT="\( \tilde{\theta }_{l}=\frac{a_{l}}{a_{l}+b_{l}} \)">. The estimates
+of the components of variance of interest for the lth locus are within
+populations, r is the number of populations examined:
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+b_{l}=2\sum ^{r}_{i=1}\frac{n_{i}\tilde{\alpha }_{il}}{r(2\bar{n}-1)}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="136" HEIGHT="53" BORDER="0"
+ SRC="img33.png"
+ ALT="\begin{displaymath}
+b_{l}=2\sum ^{r}_{i=1}\frac{n_{i}\tilde{\alpha }_{il}}{r(2\bar{n}-1)}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+and between populations:
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+a_{l}=\frac{\left[ 2\sum ^{r}_{i=1}n_{i}\sum ^{v_{l}}_{u=1}\left( \tilde{p}_{ilu}-\tilde{p}_{lu}\right) ^{2}-\left( r-1\right) b_{l}\right] }{2\left( r-1\right) n_{c}}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="330" HEIGHT="56" BORDER="0"
+ SRC="img34.png"
+ ALT="\begin{displaymath}
+a_{l}=\frac{\left[ 2\sum ^{r}_{i=1}n_{i}\sum ^{v_{l}}_{u=1}\...
+...^{2}-\left( r-1\right) b_{l}\right] }{2\left( r-1\right) n_{c}}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+When there are just two populations, r = 2, the usual genetic distance
+situation obtains, and the most convenient computing formulas for
+the variance components are (used in Populations)
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+a_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{2lu}\right) ^{2}-\frac{\left( n_{1}+n_{2}\right) \left( n_{1}\tilde{\alpha }_{1l}+n_{2}\tilde{\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="364" HEIGHT="49" BORDER="0"
+ SRC="img35.png"
+ ALT="\begin{displaymath}
+a_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{...
+...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+a_{l}+b_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tilde{p}_{2lu}\right) ^{2}+\frac{\left( 4n_{1}n_{2}-n_{1}-n_{2}\right) \left( n_{1}\tilde{\alpha }_{1l}+n_{2}\tilde{\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="456" HEIGHT="49" BORDER="0"
+ SRC="img36.png"
+ ALT="\begin{displaymath}
+a_{l}+b_{l}=\frac{1}{2}\sum _{u}\left( \tilde{p}_{1lu}-\tild...
+...\alpha }_{2l}\right) }{4n_{1}n_{2}\left( n_{1}+n_{2}-1\right) }\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node14.html b/html/old_formula/node14.html
new file mode 100755
index 0000000..b0eb5d5
--- /dev/null
+++ b/html/old_formula/node14.html
@@ -0,0 +1,82 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>weighted average of single-locus ratio estimators :</TITLE>
+<META NAME="description" CONTENT="weighted average of single-locus ratio estimators :">
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+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html198"
+ HREF="node15.html">least squares estimator :</A>
+<B> Up:</B> <A NAME="tex2html196"
+ HREF="node12.html">Reynold's genetic distance for</A>
+<B> Previous:</B> <A NAME="tex2html190"
+ HREF="node13.html">unweighted average of single-locus</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H3><A NAME="SECTION001110200000000000000">
+weighted average of single-locus ratio estimators :</A>
+</H3>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+\tilde{\theta }_{W}=\frac{\left( \sum ^{m}_{l=1}a_{l}\right) }{\sum ^{m}_{l=1}\left( a_{l}+b_{l}\right) }
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="143" HEIGHT="46" BORDER="0"
+ SRC="img37.png"
+ ALT="\begin{displaymath}
+\tilde{\theta }_{W}=\frac{\left( \sum ^{m}_{l=1}a_{l}\right) }{\sum ^{m}_{l=1}\left( a_{l}+b_{l}\right) }\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node15.html b/html/old_formula/node15.html
new file mode 100755
index 0000000..a0ce58e
--- /dev/null
+++ b/html/old_formula/node15.html
@@ -0,0 +1,139 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>least squares estimator :</TITLE>
+<META NAME="description" CONTENT="least squares estimator :">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
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+
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+
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+<LINK REL="up" HREF="node12.html">
+<LINK REL="next" HREF="node16.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html205"
+ HREF="node16.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html203"
+ HREF="node12.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html199"
+ HREF="node14.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html206"
+ HREF="node16.html">SMM distances</A>
+<B> Up:</B> <A NAME="tex2html204"
+ HREF="node12.html">Reynold's genetic distance for</A>
+<B> Previous:</B> <A NAME="tex2html200"
+ HREF="node14.html">weighted average of single-locus</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H3><A NAME="SECTION001110300000000000000">
+least squares <!-- MATH
+ $\theta \protect$
+ -->
+<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="\( \theta \)"> estimator :</A>
+</H3>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+\tilde{\theta }_{L}=\frac{2x+y-z\pm \sqrt{\left( z-y\right) ^{2}+4x^{2}}}{2\left( y-z\right) }
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="248" HEIGHT="57" BORDER="0"
+ SRC="img38.png"
+ ALT="\begin{displaymath}
+\tilde{\theta }_{L}=\frac{2x+y-z\pm \sqrt{\left( z-y\right) ^{2}+4x^{2}}}{2\left( y-z\right) }\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+where: <!-- MATH
+ $z=\sum ^{m}_{l=1}a_{l}^{2}$
+ -->
+<IMG
+ WIDTH="90" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="img39.png"
+ ALT="\( z=\sum ^{m}_{l=1}a_{l}^{2} \)">, <!-- MATH
+ $x=\sum ^{m}_{l=1}a_{l}b_{l}$
+ -->
+<IMG
+ WIDTH="100" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="img40.png"
+ ALT="\( x=\sum ^{m}_{l=1}a_{l}b_{l} \)">
+and <!-- MATH
+ $y=\sum ^{m}_{l=1}b_{l}^{2}$
+ -->
+<IMG
+ WIDTH="88" HEIGHT="33" ALIGN="MIDDLE" BORDER="0"
+ SRC="img41.png"
+ ALT="\( y=\sum ^{m}_{l=1}b_{l}^{2} \)"> .
+
+<P>
+to check which of the two solutions for <!-- MATH
+ $\tilde{\theta }_{L}$
+ -->
+<IMG
+ WIDTH="21" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img42.png"
+ ALT="\( \tilde{\theta }_{L} \)">
+provides the minimum, the residual sum of squares, R, should be calculated
+for each where:
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+R=\frac{\left( 2x+y+z\right) \tilde{\theta }_{L}^{2}-2\left( x+z\right) \tilde{\theta }_{L}+z}{1-2\tilde{\theta }_{L}+2\tilde{\theta }_{L}^{2}}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="266" HEIGHT="50" BORDER="0"
+ SRC="img43.png"
+ ALT="\begin{displaymath}
+R=\frac{\left( 2x+y+z\right) \tilde{\theta }_{L}^{2}-2\left(...
+...theta }_{L}+z}{1-2\tilde{\theta }_{L}+2\tilde{\theta }_{L}^{2}}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node16.html b/html/old_formula/node16.html
new file mode 100755
index 0000000..802badb
--- /dev/null
+++ b/html/old_formula/node16.html
@@ -0,0 +1,106 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>SMM distances</TITLE>
+<META NAME="description" CONTENT="SMM distances">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="previous" HREF="node2.html">
+<LINK REL="up" HREF="node1.html">
+<LINK REL="next" HREF="node17.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html213"
+ HREF="node17.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html211"
+ HREF="node1.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html207"
+ HREF="node15.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html214"
+ HREF="node17.html">Goldstein et al. (1995a)</A>
+<B> Up:</B> <A NAME="tex2html212"
+ HREF="node1.html">Distances</A>
+<B> Previous:</B> <A NAME="tex2html208"
+ HREF="node15.html">least squares estimator :</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00120000000000000000">
+SMM distances</A>
+</H1>
+
+<P>
+<!-- MATH
+ $\mu _{X_{j}}=\sum _{i}ix_{ij}$
+ -->
+<IMG
+ WIDTH="103" HEIGHT="31" ALIGN="MIDDLE" BORDER="0"
+ SRC="img44.png"
+ ALT="\( \mu _{X_{j}}=\sum _{i}ix_{ij} \)"> and <!-- MATH
+ $\mu _{Y_{j}}=\sum _{i}iy_{ij}$
+ -->
+<IMG
+ WIDTH="98" HEIGHT="31" ALIGN="MIDDLE" BORDER="0"
+ SRC="img45.png"
+ ALT="\( \mu _{Y_{j}}=\sum _{i}iy_{ij} \)">
+are average allelic states at the <I>j</I>th locus, and <IMG
+ WIDTH="24" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="img5.png"
+ ALT="\( x_{ij} \)">
+and <IMG
+ WIDTH="23" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="img6.png"
+ ALT="\( y_{ij} \)"> are the frequencies of the allele in state <IMG
+ WIDTH="10" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img46.png"
+ ALT="\( i \)">
+at the <I>j</I>th locus in populations X an Y, respectively.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html215"
+ HREF="node17.html">Goldstein et al. (1995a) [Goldstein, D.B. 97]</A>
+<LI><A NAME="tex2html216"
+ HREF="node18.html">average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995)
+[Goldstein, D.B. 97]</A>
+<LI><A NAME="tex2html217"
+ HREF="node19.html">Shriver et al.'s (1995) [Shriver, M.D. 95]</A>
+<LI><A NAME="tex2html218"
+ HREF="node20.html">Lev A. Zhivotovsky (1999) [Takezaki, N. 96]</A>
+</UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node17.html b/html/old_formula/node17.html
new file mode 100755
index 0000000..404b4bf
--- /dev/null
+++ b/html/old_formula/node17.html
@@ -0,0 +1,83 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Goldstein et al. (1995a) [Goldstein, D.B. 97]</TITLE>
+<META NAME="description" CONTENT="Goldstein et al. (1995a) [Goldstein, D.B. 97]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node18.html">
+<LINK REL="previous" HREF="node16.html">
+<LINK REL="up" HREF="node16.html">
+<LINK REL="next" HREF="node18.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html227"
+ HREF="node18.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html225"
+ HREF="node16.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html219"
+ HREF="node16.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html228"
+ HREF="node18.html">average square distance (ASD)</A>
+<B> Up:</B> <A NAME="tex2html226"
+ HREF="node16.html">SMM distances</A>
+<B> Previous:</B> <A NAME="tex2html220"
+ HREF="node16.html">SMM distances</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00121000000000000000">
+Goldstein et al. (1995a) [<A
+ HREF="node21.html#GP97">Goldstein, D.B. 97</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+\left( \delta \mu \right) ^{2}=\frac{\sum ^{r}_{j}\left( \mu _{X_{j}}-\mu _{Y_{j}}\right) ^{2}}{r}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="178" HEIGHT="47" BORDER="0"
+ SRC="img47.png"
+ ALT="\begin{displaymath}
+\left( \delta \mu \right) ^{2}=\frac{\sum ^{r}_{j}\left( \mu _{X_{j}}-\mu _{Y_{j}}\right) ^{2}}{r}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node18.html b/html/old_formula/node18.html
new file mode 100755
index 0000000..80bcfd2
--- /dev/null
+++ b/html/old_formula/node18.html
@@ -0,0 +1,86 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995)
+[Goldstein, D.B. 97]</TITLE>
+<META NAME="description" CONTENT="average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995)
+[Goldstein, D.B. 97]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node19.html">
+<LINK REL="previous" HREF="node17.html">
+<LINK REL="up" HREF="node16.html">
+<LINK REL="next" HREF="node19.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html237"
+ HREF="node19.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html235"
+ HREF="node16.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html229"
+ HREF="node17.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html238"
+ HREF="node19.html">Shriver et al.'s (1995)</A>
+<B> Up:</B> <A NAME="tex2html236"
+ HREF="node16.html">SMM distances</A>
+<B> Previous:</B> <A NAME="tex2html230"
+ HREF="node17.html">Goldstein et al. (1995a)</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00122000000000000000">
+average square distance (ASD) (Goldstein et al. 1995b; Slatkin 1995)
+[<A
+ HREF="node21.html#GP97">Goldstein, D.B. 97</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+ASD=\frac{\sum ^{r}_{k}\sum _{i,j}\left( \left( i-j\right) ^{2}x_{ik}y_{jk}\right) }{r}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="238" HEIGHT="52" BORDER="0"
+ SRC="img48.png"
+ ALT="\begin{displaymath}
+ASD=\frac{\sum ^{r}_{k}\sum _{i,j}\left( \left( i-j\right) ^{2}x_{ik}y_{jk}\right) }{r}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node19.html b/html/old_formula/node19.html
new file mode 100755
index 0000000..d1c94e1
--- /dev/null
+++ b/html/old_formula/node19.html
@@ -0,0 +1,106 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Shriver et al.'s (1995) [Shriver, M.D. 95]</TITLE>
+<META NAME="description" CONTENT="Shriver et al.'s (1995) [Shriver, M.D. 95]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node20.html">
+<LINK REL="previous" HREF="node18.html">
+<LINK REL="up" HREF="node16.html">
+<LINK REL="next" HREF="node20.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html247"
+ HREF="node20.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html245"
+ HREF="node16.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html239"
+ HREF="node18.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html248"
+ HREF="node20.html">Lev A. Zhivotovsky (1999)</A>
+<B> Up:</B> <A NAME="tex2html246"
+ HREF="node16.html">SMM distances</A>
+<B> Previous:</B> <A NAME="tex2html240"
+ HREF="node18.html">average square distance (ASD)</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00123000000000000000">
+Shriver et al.'s (1995) [<A
+ HREF="node21.html#SJB95">Shriver, M.D. 95</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+D_{SW}=W_{XY}-\frac{\left( W_{X}+W_{Y}\right) }{2}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="201" HEIGHT="40" BORDER="0"
+ SRC="img49.png"
+ ALT="\begin{displaymath}
+D_{SW}=W_{XY}-\frac{\left( W_{X}+W_{Y}\right) }{2}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+where <!-- MATH
+ $W_{X}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left| i-j\right| x_{ik}x_{jk}\right) }{r}$
+ -->
+<IMG
+ WIDTH="193" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="img50.png"
+ ALT="\( W_{X}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}x_{jk}\right) }{r} \)">,
+<!-- MATH
+ $W_{Y}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left| i-j\right| y_{ik}y_{jk}\right) }{r}$
+ -->
+<IMG
+ WIDTH="190" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="img51.png"
+ ALT="\( W_{Y}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert y_{ik}y_{jk}\right) }{r} \)">,
+<!-- MATH
+ $W_{XY}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left| i-j\right| x_{ik}y_{jk}\right) }{r}$
+ -->
+<IMG
+ WIDTH="202" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="img52.png"
+ ALT="\( W_{XY}=\frac{\sum ^{r}_{k}\sum _{i\neq j}\left( \left\vert i-j\right\vert x_{ik}y_{jk}\right) }{r} \)">
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node2.html b/html/old_formula/node2.html
new file mode 100755
index 0000000..63317c6
--- /dev/null
+++ b/html/old_formula/node2.html
@@ -0,0 +1,159 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>IAM distances</TITLE>
+<META NAME="description" CONTENT="IAM distances">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node16.html">
+<LINK REL="previous" HREF="node1.html">
+<LINK REL="up" HREF="node1.html">
+<LINK REL="next" HREF="node3.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html63"
+ HREF="node3.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html61"
+ HREF="node1.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html55"
+ HREF="node1.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html64"
+ HREF="node3.html">Shared allele distance (Chakraborty</A>
+<B> Up:</B> <A NAME="tex2html62"
+ HREF="node1.html">Distances</A>
+<B> Previous:</B> <A NAME="tex2html56"
+ HREF="node1.html">Distances</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00110000000000000000">
+IAM distances</A>
+</H1>
+
+<P>
+<!-- MATH
+ $J_{X}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x^{2}_{ij}}{r}$
+ -->
+<IMG
+ WIDTH="128" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="img2.png"
+ ALT="\( J_{X}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x^{2}_{ij}}{r} \)"> and
+<!-- MATH
+ $J_{Y}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}y^{2}_{ij}}{r}$
+ -->
+<IMG
+ WIDTH="127" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="img3.png"
+ ALT="\( J_{Y}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}y^{2}_{ij}}{r} \)">are
+the average homozygoties over loci in populations X and Y, respectively,
+and <!-- MATH
+ $J_{XY}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x_{ij}y_{ij}}{r}$
+ -->
+<IMG
+ WIDTH="155" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="img4.png"
+ ALT="\( J_{XY}=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}x_{ij}y_{ij}}{r} \)">.
+
+<P>
+<IMG
+ WIDTH="24" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="img5.png"
+ ALT="\( x_{ij} \)"> and <IMG
+ WIDTH="23" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="img6.png"
+ ALT="\( y_{ij} \)"> are the frequencies of the <I>i</I>th
+allele at the <I>j</I>th locus in populations X and Y, respectively,
+<IMG
+ WIDTH="25" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="img7.png"
+ ALT="\( m_{j} \)"> is the number of alleles at the <I>j</I>th locus, and
+r is the number of loci examined.
+
+<P>
+<BR><HR>
+<!--Table of Child-Links-->
+<A NAME="CHILD_LINKS"><STRONG>Subsections</STRONG></A>
+
+<UL>
+<LI><A NAME="tex2html65"
+ HREF="node3.html">Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]</A>
+<LI><A NAME="tex2html66"
+ HREF="node4.html">Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html67"
+ HREF="node5.html">Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html68"
+ HREF="node6.html">Latter's (1972) Fst (=<IMG
+ WIDTH="14" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img16.png"
+ ALT="\( \phi \protect \)">*) distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html69"
+ HREF="node7.html">Rogers' (1972) distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html70"
+ HREF="node8.html">Prevosti et al's (1975) distance [Takezaki, N. 96] has a statistical property
+similar to that of Dr and is defined as</A>
+<LI><A NAME="tex2html71"
+ HREF="node9.html">Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html72"
+ HREF="node10.html">Nei et al's (1983) <IMG
+ WIDTH="28" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img21.png"
+ ALT="\( D_{A}\protect \)"> distance [Takezaki, N. 96]</A>
+<LI><A NAME="tex2html73"
+ HREF="node11.html">Sanghvi's (1953) <IMG
+ WIDTH="26" HEIGHT="16" ALIGN="BOTTOM" BORDER="0"
+ SRC="img23.png"
+ ALT="\( X^{2}\protect \)"> distance[Takezaki, N. 96]</A>
+<LI><A NAME="tex2html74"
+ HREF="node12.html">Reynold's genetic distance for short-term evolution (1983) [Reynolds, J. 83]</A>
+<UL>
+<LI><A NAME="tex2html75"
+ HREF="node13.html">unweighted average of single-locus ratio estimators, <!-- MATH
+ $\tilde{\theta }_{U}\protect$
+ -->
+<IMG
+ WIDTH="22" HEIGHT="37" ALIGN="MIDDLE" BORDER="0"
+ SRC="img30.png"
+ ALT="\( \tilde{\theta }_{U}\protect \)">:</A>
+<LI><A NAME="tex2html76"
+ HREF="node14.html">weighted average of single-locus ratio estimators :</A>
+<LI><A NAME="tex2html77"
+ HREF="node15.html">least squares <!-- MATH
+ $\theta \protect$
+ -->
+<IMG
+ WIDTH="12" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
+ SRC="img1.png"
+ ALT="\( \theta \)"> estimator :</A>
+</UL></UL>
+<!--End of Table of Child-Links-->
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node20.html b/html/old_formula/node20.html
new file mode 100755
index 0000000..da9c061
--- /dev/null
+++ b/html/old_formula/node20.html
@@ -0,0 +1,145 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Lev A. Zhivotovsky (1999) [Takezaki, N. 96]</TITLE>
+<META NAME="description" CONTENT="Lev A. Zhivotovsky (1999) [Takezaki, N. 96]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
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+
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+ SRC="/usr/share/latex2html/icons/up.png"></A>
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+ SRC="/usr/share/latex2html/icons/prev.png"></A>
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+<B> Next:</B> <A NAME="tex2html256"
+ HREF="node21.html">Bibliography</A>
+<B> Up:</B> <A NAME="tex2html254"
+ HREF="node16.html">SMM distances</A>
+<B> Previous:</B> <A NAME="tex2html250"
+ HREF="node19.html">Shriver et al.'s (1995)</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00124000000000000000">
+Lev A. Zhivotovsky (1999) [<A
+ HREF="node21.html#TN96">Takezaki, N. 96</A>]</A>
+</H2>
+
+<P>
+Consider two populations, X an Y and r autosomal microsatellite loci.<!-- MATH
+ $\overline{\mu _{X}}$
+ -->
+<IMG
+ WIDTH="26" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="img53.png"
+ ALT="\( \overline{\mu _{X}} \)">
+and <!-- MATH
+ $\overline{\mu _{Y}}$
+ -->
+<IMG
+ WIDTH="25" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="img54.png"
+ ALT="\( \overline{\mu _{Y}} \)">are the mean of <IMG
+ WIDTH="31" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="img55.png"
+ ALT="\( \mu _{X_{j}} \)">and
+<IMG
+ WIDTH="28" HEIGHT="28" ALIGN="MIDDLE" BORDER="0"
+ SRC="img56.png"
+ ALT="\( \mu _{Y_{j}} \)">averall loci for population X and Y respectively.
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+D_{R}=-\log \left( \frac{C_{XY}}{V_{XY}}\right)
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="141" HEIGHT="45" BORDER="0"
+ SRC="img57.png"
+ ALT="\begin{displaymath}
+D_{R}=-\log \left( \frac{C_{XY}}{V_{XY}}\right) \end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+with,
+
+<P>
+<!-- MATH
+ $C_{XY}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}\mu _{Y_{j}}-r\overline{\mu _{X}}\overline{\mu _{Y}}\right)$
+ -->
+<IMG
+ WIDTH="253" HEIGHT="44" ALIGN="MIDDLE" BORDER="0"
+ SRC="img58.png"
+ ALT="\( C_{XY}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}\mu _{Y_{j}}-r\overline{\mu _{X}}\overline{\mu _{Y}}\right) \)">
+and <!-- MATH
+ $V_{XY}=\frac{1}{2}\left( V_{X}+V_{Y}\right)$
+ -->
+<IMG
+ WIDTH="143" HEIGHT="34" ALIGN="MIDDLE" BORDER="0"
+ SRC="img59.png"
+ ALT="\( V_{XY}=\frac{1}{2}\left( V_{X}+V_{Y}\right) \)">, where <!-- MATH
+ $V_{X}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}^{2}-r\overline{\mu _{X}}^{2}\right)$
+ -->
+<IMG
+ WIDTH="204" HEIGHT="44" ALIGN="MIDDLE" BORDER="0"
+ SRC="img60.png"
+ ALT="\( V_{X}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{X_{j}}^{2}-r\overline{\mu _{X}}^{2}\right) \)">,<!-- MATH
+ $V_{Y}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{Y_{j}}^{2}-r\overline{\mu _{Y}}^{2}\right)$
+ -->
+<IMG
+ WIDTH="199" HEIGHT="44" ALIGN="MIDDLE" BORDER="0"
+ SRC="img61.png"
+ ALT="\( V_{Y}=\frac{1}{r-1}\left( \sum ^{r}_{j}\mu _{Y_{j}}^{2}-r\overline{\mu _{Y}}^{2}\right) \)">
+
+<P>
+Attention, to avoid software crash, when <IMG
+ WIDTH="67" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img62.png"
+ ALT="\( C_{XY}<1 \)">, <IMG
+ WIDTH="38" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img63.png"
+ ALT="\( C_{XY} \)">
+is set to 1.
+
+<P>
+
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node21.html b/html/old_formula/node21.html
new file mode 100755
index 0000000..61fd3d6
--- /dev/null
+++ b/html/old_formula/node21.html
@@ -0,0 +1,102 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Bibliography</TITLE>
+<META NAME="description" CONTENT="Bibliography">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
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+ HREF="formules.html">formules</A>
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+ HREF="node20.html">Lev A. Zhivotovsky (1999)</A>
+<BR><BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00200000000000000000">
+Bibliography</A>
+</H2><DL COMPACT><DD><P></P><DT><A NAME="GP97">Goldstein, D.B. 97</A>
+<DD>
+Goldstein, D.B. & Pollock, D.D.
+<BR><EM>Launching Microsatellites: A Review of Mutation Processes and
+ Methods of Phylogenetic Inference</EM>.
+<BR>Journal of Heredity, vol. 88, no. 335-342, pages 0022-1503, 31 1997.
+<BR>1997.
+
+<P></P><DT><A NAME="JC93">Jin, L. 93</A>
+<DD>
+Jin, L. & Chakraborty, R.
+<BR><EM>Estimation of Genetic Distance and Coefficient of Gene
+ Diversity from Single-Probe Multilocus DNA Fingerprinting
+ Data</EM>.
+<BR>Mol. Biol. Evol., vol. 11, no. 1, pages 120-127, 13 1993.
+<BR>1994.
+
+<P></P><DT><A NAME="RWC83">Reynolds, J. 83</A>
+<DD>
+Reynolds, J., Weir, B.S. & Cockerham, C.
+<BR><EM>Estimation of the coancestry coefficient: basis for a short-term
+ genetic distance</EM>.
+<BR>Genetics Society of America, vol. 105, pages 767-779, November 1983.
+<BR>1983.
+
+<P></P><DT><A NAME="SJB95">Shriver, M.D. 95</A>
+<DD>
+Shriver, M.D., Jin, L. & Boerwinkle, E.
+<BR><EM>A Novel Measure of Genetic Distance for Highly Polymorphic
+ Tandem Repeat Loci</EM>.
+<BR>Mol. Bio. Evol., vol. 12, no. 5, pages 914-920, 4 1995.
+
+<P></P><DT><A NAME="TN96">Takezaki, N. 96</A>
+<DD>
+Takezaki, N. & Nei, M.
+<BR><EM>Genetic Distances and Reconstruction of Phylogenetic
+ Trees From Microsatellite DNA</EM>.
+<BR>Genetics, no. 144, pages 189-399, 6 1996.
+<BR>september, 1996.
+</DL>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node22.html b/html/old_formula/node22.html
new file mode 100755
index 0000000..144164a
--- /dev/null
+++ b/html/old_formula/node22.html
@@ -0,0 +1,73 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>About this document ...</TITLE>
+<META NAME="description" CONTENT="About this document ...">
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+<BR>
+<!--End of Navigation Panel-->
+
+<H1><A NAME="SECTION00300000000000000000">
+About this document ...</A>
+</H1>
+ <P>
+This document was generated using the
+<A HREF="http://www-texdev.mpce.mq.edu.au/l2h/docs/manual/"><STRONG>LaTeX</STRONG>2<tt>HTML</tt></A> translator Version 2K.1beta (1.48)
+<P>
+Copyright © 1993, 1994, 1995, 1996,
+<A HREF="http://cbl.leeds.ac.uk/nikos/personal.html">Nikos Drakos</A>,
+Computer Based Learning Unit, University of Leeds.
+<BR>
+Copyright © 1997, 1998, 1999,
+<A HREF="http://www.maths.mq.edu.au/~ross/">Ross Moore</A>,
+Mathematics Department, Macquarie University, Sydney.
+<P>
+The command line arguments were: <BR>
+ <STRONG>latex2html</STRONG> <TT><A NAME="tex2html1"
+ HREF="../formules.tex">formules.tex</A></TT>
+<P>
+The translation was initiated by Olivier Langella on 2002-03-20
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+Olivier Langella
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+</HTML>
diff --git a/html/old_formula/node3.html b/html/old_formula/node3.html
new file mode 100755
index 0000000..42802f6
--- /dev/null
+++ b/html/old_formula/node3.html
@@ -0,0 +1,131 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]</TITLE>
+<META NAME="description" CONTENT="Shared allele distance (Chakraborty and Jin, 1993) [Jin, L. 93]">
+<META NAME="keywords" CONTENT="formules">
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+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html87"
+ HREF="node4.html">Nei's (1972) standard genetic</A>
+<B> Up:</B> <A NAME="tex2html85"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html79"
+ HREF="node2.html">IAM distances</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00111000000000000000">
+Shared allele distance (Chakraborty and Jin, 1993) [<A
+ HREF="node21.html#JC93">Jin, L. 93</A>]</A>
+</H2>
+
+<P>
+between individuals:
+
+<P>
+<!-- MATH
+ $D_{SA_{I}}=1-P_{SA_{I}}$
+ -->
+<IMG
+ WIDTH="127" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img8.png"
+ ALT="\( D_{SA_{I}}=1-P_{SA_{I}} \)">, with <!-- MATH
+ $P_{SA_{I}}=\frac{\sum ^{r}_{j}S}{2r}$
+ -->
+<IMG
+ WIDTH="98" HEIGHT="54" ALIGN="MIDDLE" BORDER="0"
+ SRC="img9.png"
+ ALT="\( P_{SA_{I}}=\frac{\sum ^{r}_{j}S}{2r} \)">
+
+<P>
+where the number of shared alleles S is sumed over all loci r.
+
+<P>
+between populations:
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+D_{SA_{B}}=1-\frac{2\overline{P}_{SA_{B}}}{\overline{P}_{SA_{X}}+\overline{P}_{SA_{Y}}}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="194" HEIGHT="48" BORDER="0"
+ SRC="img10.png"
+ ALT="\begin{displaymath}
+D_{SA_{B}}=1-\frac{2\overline{P}_{SA_{B}}}{\overline{P}_{SA_{X}}+\overline{P}_{SA_{Y}}}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+where the average proportion of shared alleles between and within
+populations X and Y (<!-- MATH
+ $\overline{P}_{SA_{B}}$
+ -->
+<IMG
+ WIDTH="45" HEIGHT="35" ALIGN="MIDDLE" BORDER="0"
+ SRC="img11.png"
+ ALT="\( \overline{P}_{SA_{B}} \)">, <!-- MATH
+ $\overline{P}_{SA_{X}}$
+ -->
+<IMG
+ WIDTH="46" HEIGHT="35" ALIGN="MIDDLE" BORDER="0"
+ SRC="img12.png"
+ ALT="\( \overline{P}_{SA_{X}} \)">,<!-- MATH
+ $\overline{P}_{SA_{Y}}$
+ -->
+<IMG
+ WIDTH="45" HEIGHT="35" ALIGN="MIDDLE" BORDER="0"
+ SRC="img13.png"
+ ALT="\( \overline{P}_{SA_{Y}} \)">
+respectively) is computed overall possible combinations of individuals
+sampled.
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node4.html b/html/old_formula/node4.html
new file mode 100755
index 0000000..e57d7b6
--- /dev/null
+++ b/html/old_formula/node4.html
@@ -0,0 +1,83 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]</TITLE>
+<META NAME="description" CONTENT="Nei's (1972) standard genetic distance (Ds) [Takezaki, N. 96]">
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+<A NAME="tex2html88"
+ HREF="node3.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html97"
+ HREF="node5.html">Nei's (1973) minimum genetic</A>
+<B> Up:</B> <A NAME="tex2html95"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html89"
+ HREF="node3.html">Shared allele distance (Chakraborty</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00112000000000000000">
+Nei's (1972) standard genetic distance (Ds) [<A
+ HREF="node21.html#TN96">Takezaki, N. 96</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+Ds=-\ln \left[ \frac{J_{XY}}{\sqrt{J_{X}J_{Y}}}\right]
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="144" HEIGHT="45" BORDER="0"
+ SRC="img14.png"
+ ALT="\begin{displaymath}
+Ds=-\ln \left[ \frac{J_{XY}}{\sqrt{J_{X}J_{Y}}}\right] \end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node5.html b/html/old_formula/node5.html
new file mode 100755
index 0000000..414424a
--- /dev/null
+++ b/html/old_formula/node5.html
@@ -0,0 +1,83 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]</TITLE>
+<META NAME="description" CONTENT="Nei's (1973) minimum genetic distance (Dm) [Takezaki, N. 96]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node6.html">
+<LINK REL="previous" HREF="node4.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node6.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html106"
+ HREF="node6.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html104"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html98"
+ HREF="node4.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html107"
+ HREF="node6.html">Latter's (1972) Fst (=*)</A>
+<B> Up:</B> <A NAME="tex2html105"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html99"
+ HREF="node4.html">Nei's (1972) standard genetic</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00113000000000000000">
+Nei's (1973) minimum genetic distance (Dm) [<A
+ HREF="node21.html#TN96">Takezaki, N. 96</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+Dm=\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="175" HEIGHT="40" BORDER="0"
+ SRC="img15.png"
+ ALT="\begin{displaymath}
+Dm=\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node6.html b/html/old_formula/node6.html
new file mode 100755
index 0000000..14b14af
--- /dev/null
+++ b/html/old_formula/node6.html
@@ -0,0 +1,86 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Latter's (1972) Fst (=*) distance [Takezaki, N. 96]</TITLE>
+<META NAME="description" CONTENT="Latter's (1972) Fst (=*) distance [Takezaki, N. 96]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node7.html">
+<LINK REL="previous" HREF="node5.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node7.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html116"
+ HREF="node7.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html114"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html108"
+ HREF="node5.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html117"
+ HREF="node7.html">Rogers' (1972) distance [Takezaki,</A>
+<B> Up:</B> <A NAME="tex2html115"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html109"
+ HREF="node5.html">Nei's (1973) minimum genetic</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00114000000000000000">
+Latter's (1972) Fst (=<IMG
+ WIDTH="14" HEIGHT="29" ALIGN="MIDDLE" BORDER="0"
+ SRC="img16.png"
+ ALT="\( \phi \protect \)">*) distance [<A
+ HREF="node21.html#TN96">Takezaki, N. 96</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+Fst=\frac{\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}}{1-J_{XY}}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="156" HEIGHT="48" BORDER="0"
+ SRC="img17.png"
+ ALT="\begin{displaymath}
+Fst=\frac{\frac{\left( J_{X}+J_{Y}\right) }{2}-J_{XY}}{1-J_{XY}}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node7.html b/html/old_formula/node7.html
new file mode 100755
index 0000000..9efd603
--- /dev/null
+++ b/html/old_formula/node7.html
@@ -0,0 +1,83 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Rogers' (1972) distance [Takezaki, N. 96]</TITLE>
+<META NAME="description" CONTENT="Rogers' (1972) distance [Takezaki, N. 96]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node8.html">
+<LINK REL="previous" HREF="node6.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node8.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html126"
+ HREF="node8.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html124"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html118"
+ HREF="node6.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html127"
+ HREF="node8.html">Prevosti et al's (1975)</A>
+<B> Up:</B> <A NAME="tex2html125"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html119"
+ HREF="node6.html">Latter's (1972) Fst (=*)</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00115000000000000000">
+Rogers' (1972) distance [<A
+ HREF="node21.html#TN96">Takezaki, N. 96</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+Dr=\frac{1}{r}\sum ^{r}_{j}\sqrt{\frac{\sum ^{m}_{i}\left( x_{ij}-y_{ij}\right) ^{2}}{2}}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="212" HEIGHT="63" BORDER="0"
+ SRC="img18.png"
+ ALT="\begin{displaymath}
+Dr=\frac{1}{r}\sum ^{r}_{j}\sqrt{\frac{\sum ^{m}_{i}\left( x_{ij}-y_{ij}\right) ^{2}}{2}}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node8.html b/html/old_formula/node8.html
new file mode 100755
index 0000000..771281d
--- /dev/null
+++ b/html/old_formula/node8.html
@@ -0,0 +1,86 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Prevosti et al's (1975) distance [Takezaki, N. 96] has a statistical property
+similar to that of Dr and is defined as</TITLE>
+<META NAME="description" CONTENT="Prevosti et al's (1975) distance [Takezaki, N. 96] has a statistical property
+similar to that of Dr and is defined as">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node9.html">
+<LINK REL="previous" HREF="node7.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node9.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html136"
+ HREF="node9.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html134"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html128"
+ HREF="node7.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html137"
+ HREF="node9.html">Cavali-Sforza and Edwards' (1967)</A>
+<B> Up:</B> <A NAME="tex2html135"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html129"
+ HREF="node7.html">Rogers' (1972) distance [Takezaki,</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00116000000000000000">
+Prevosti et al's (1975) distance [<A
+ HREF="node21.html#TN96">Takezaki, N. 96</A>] has a statistical property
+similar to that of Dr and is defined as</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+Cp=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}\left| x_{ij}-y_{ij}\right| }{2r}
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="176" HEIGHT="44" BORDER="0"
+ SRC="img19.png"
+ ALT="\begin{displaymath}
+Cp=\frac{\sum ^{r}_{j}\sum ^{m_{j}}_{i}\left\vert x_{ij}-y_{ij}\right\vert }{2r}\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/node9.html b/html/old_formula/node9.html
new file mode 100755
index 0000000..8bbceab
--- /dev/null
+++ b/html/old_formula/node9.html
@@ -0,0 +1,83 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
+
+<!--Converted with LaTeX2HTML 2K.1beta (1.48)
+original version by: Nikos Drakos, CBLU, University of Leeds
+* revised and updated by: Marcus Hennecke, Ross Moore, Herb Swan
+* with significant contributions from:
+ Jens Lippmann, Marek Rouchal, Martin Wilck and others -->
+<HTML>
+<HEAD>
+<TITLE>Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96]</TITLE>
+<META NAME="description" CONTENT="Cavali-Sforza and Edwards' (1967) chord distance [Takezaki, N. 96]">
+<META NAME="keywords" CONTENT="formules">
+<META NAME="resource-type" CONTENT="document">
+<META NAME="distribution" CONTENT="global">
+
+<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
+<META NAME="Generator" CONTENT="LaTeX2HTML v2K.1beta">
+<META HTTP-EQUIV="Content-Style-Type" CONTENT="text/css">
+
+<LINK REL="STYLESHEET" HREF="formules.css">
+
+<LINK REL="next" HREF="node10.html">
+<LINK REL="previous" HREF="node8.html">
+<LINK REL="up" HREF="node2.html">
+<LINK REL="next" HREF="node10.html">
+</HEAD>
+
+<BODY >
+<!--Navigation Panel-->
+<A NAME="tex2html146"
+ HREF="node10.html">
+<IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next"
+ SRC="/usr/share/latex2html/icons/next.png"></A>
+<A NAME="tex2html144"
+ HREF="node2.html">
+<IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up"
+ SRC="/usr/share/latex2html/icons/up.png"></A>
+<A NAME="tex2html138"
+ HREF="node8.html">
+<IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous"
+ SRC="/usr/share/latex2html/icons/prev.png"></A>
+<BR>
+<B> Next:</B> <A NAME="tex2html147"
+ HREF="node10.html">Nei et al's (1983)</A>
+<B> Up:</B> <A NAME="tex2html145"
+ HREF="node2.html">IAM distances</A>
+<B> Previous:</B> <A NAME="tex2html139"
+ HREF="node8.html">Prevosti et al's (1975)</A>
+<BR>
+<BR>
+<!--End of Navigation Panel-->
+
+<H2><A NAME="SECTION00117000000000000000">
+Cavali-Sforza and Edwards' (1967) chord distance [<A
+ HREF="node21.html#TN96">Takezaki, N. 96</A>]</A>
+</H2>
+
+<P>
+<BR><P></P>
+<DIV ALIGN="CENTER">
+<!-- MATH
+ \begin{displaymath}
+Dc=\frac{2}{\Pi r}\sum ^{r}_{j}\sqrt{2\left( (1-\sum _{i}^{m_{j}}\sqrt{x_{ij}y_{ij}}\right) }
+\end{displaymath}
+ -->
+
+<IMG
+ WIDTH="258" HEIGHT="64" BORDER="0"
+ SRC="img20.png"
+ ALT="\begin{displaymath}
+Dc=\frac{2}{\Pi r}\sum ^{r}_{j}\sqrt{2\left( (1-\sum _{i}^{m_{j}}\sqrt{x_{ij}y_{ij}}\right) }\end{displaymath}">
+</DIV>
+<BR CLEAR="ALL">
+<P></P>
+
+<P>
+<BR><HR>
+<ADDRESS>
+Olivier Langella
+2002-03-20
+</ADDRESS>
+</BODY>
+</HTML>
diff --git a/html/old_formula/previous_motif.gif b/html/old_formula/previous_motif.gif
new file mode 100755
index 0000000..aef90f1
Binary files /dev/null and b/html/old_formula/previous_motif.gif differ
diff --git a/html/old_formula/previous_motif_gr.gif b/html/old_formula/previous_motif_gr.gif
new file mode 100755
index 0000000..c6acaab
Binary files /dev/null and b/html/old_formula/previous_motif_gr.gif differ
diff --git a/html/old_formula/up_motif.gif b/html/old_formula/up_motif.gif
new file mode 100755
index 0000000..3d1aebf
Binary files /dev/null and b/html/old_formula/up_motif.gif differ
diff --git a/html/old_formula/up_motif_gr.gif b/html/old_formula/up_motif_gr.gif
new file mode 100755
index 0000000..a8b463a
Binary files /dev/null and b/html/old_formula/up_motif_gr.gif differ
diff --git a/html/old_formula/warnings b/html/old_formula/warnings
new file mode 100755
index 0000000..7dbc37d
--- /dev/null
+++ b/html/old_formula/warnings
@@ -0,0 +1,9 @@
+No implementation found for style `fontenc'
+
+? brace missing for \setlength
+
+? brace missing for \setlength
+
+? brace missing for \setlength
+
+? brace missing for \setlength
diff --git a/populations-1.2.32.tar.gz b/populations-1.2.32.tar.gz
new file mode 100644
index 0000000..cc7e4cc
Binary files /dev/null and b/populations-1.2.32.tar.gz differ
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index f8c5dad..101cc91 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -1,40 +1,40 @@
-
-# this command finds Qt4 libraries and sets all required variables
-# note that it's Qt4, not QT4 or qt4
-#/usr/share/cmake-2.6/Modules/FindQt4.cmake
-SET (QT_USE_QTXML true)
-FIND_PACKAGE( Qt4 REQUIRED )
-
-INCLUDE( ${QT_USE_FILE} )
-
-#FIND_PACKAGE(X11 REQUIRED)
-#FIND_PACKAGE(FindThreads REQUIRED)
-
-IF(WIN32)
- ADD_DEFINITIONS(-DMINGW32)
-ENDIF(WIN32)
-
-#INCLUDE_DIRECTORIES(X11_INCLUDE_DIR)
-# X11_FOUND is true if X11 is available.
-# * X11_INCLUDE_DIR contains the include directories to use X11.
-# * X11_LIBRARIES points to the libraries to link against to use X11.
-# Make sure the compiler can find include files from our Hello library.
-#include_directories (${X11_INCLUDE_DIR})
-
-# -m -pthread FindThreads
-
-
-# Make sure the linker can find the Hello library once it is built.
-#link_directories (${X11_INCLUDE_DIR})
-
-add_executable (populations populations.cpp distgnt jeupopexp fstat jeupop applpop applpopulations matrices applications
-arbre arbreplus couleur vecteurs locus allele individu strucpop chaineficpop metapop population)
-
-
-IF(WIN32)
- target_link_libraries (populations ${QT_LIBRARIES} m)
-ELSE(WIN32)
- target_link_libraries (populations ${QT_LIBRARIES} m)
-ENDIF(WIN32)
-
+
+# this command finds Qt4 libraries and sets all required variables
+# note that it's Qt4, not QT4 or qt4
+#/usr/share/cmake-2.6/Modules/FindQt4.cmake
+SET (QT_USE_QTXML true)
+FIND_PACKAGE( Qt4 REQUIRED )
+
+INCLUDE( ${QT_USE_FILE} )
+
+#FIND_PACKAGE(X11 REQUIRED)
+#FIND_PACKAGE(FindThreads REQUIRED)
+
+IF(WIN32)
+ ADD_DEFINITIONS(-DMINGW32)
+ENDIF(WIN32)
+
+#INCLUDE_DIRECTORIES(X11_INCLUDE_DIR)
+# X11_FOUND is true if X11 is available.
+# * X11_INCLUDE_DIR contains the include directories to use X11.
+# * X11_LIBRARIES points to the libraries to link against to use X11.
+# Make sure the compiler can find include files from our Hello library.
+#include_directories (${X11_INCLUDE_DIR})
+
+# -m -pthread FindThreads
+
+
+# Make sure the linker can find the Hello library once it is built.
+#link_directories (${X11_INCLUDE_DIR})
+
+add_executable (populations populations.cpp distgnt.cpp jeupopexp.cpp fstat.cpp jeupop.cpp applpop.cpp applpopulations.cpp matrices.cpp applications.cpp
+arbre.cpp arbreplus.cpp couleur.cpp vecteurs.cpp locus.cpp allele.cpp individu.cpp strucpop.cpp chaineficpop.cpp metapop.cpp population.cpp)
+
+
+IF(WIN32)
+ target_link_libraries (populations ${QT_LIBRARIES})
+ELSE(WIN32)
+ target_link_libraries (populations ${QT_LIBRARIES} m)
+ENDIF(WIN32)
+
\ No newline at end of file
diff --git a/src/arbre.cpp b/src/arbre.cpp
index 610dfb8..52659f3 100644
--- a/src/arbre.cpp
+++ b/src/arbre.cpp
@@ -958,7 +958,7 @@ void Arbre::reset() {
_Pracine = 0;
}
-template<class T> void Arbre::iNeighborJoining(Matrice<T> & distances) {
+void Arbre::iNeighborJoining(Matrice & distances) {
//cerr << "nj" << endl;
//pour accelerer le traitement des bootstrap:
// if (_PtabPnoeud == 0) _PtabPnoeud = new vector<Noeud *>;
@@ -972,12 +972,12 @@ template<class T> void Arbre::iNeighborJoining(Matrice<T> & distances) {
long nblignemat;
long taille(distances.GetNL());
long i, j, pos1(0), pos2(0), pos3, id, jd, refi, refj;
- T sumbr1, sumbr2;
- T comparer;
- T critere;
- T * Ptab(distances._tab);
- vector<T> accDistances;
- T distance;
+ long double sumbr1, sumbr2;
+ long double comparer;
+ long double critere;
+ long double * Ptab(distances._tab);
+ vector<long double> accDistances;
+ long double distance;
ArbreNdNoeud * Pnoeud;
@@ -1097,7 +1097,7 @@ template<class T> void Arbre::iNeighborJoining(Matrice<T> & distances) {
if ((etatMat[i]) && (i != pos1)) {
// distances.GetCase(pos1,i) = (distances.GetCase(pos1,i) + distances.GetCase(pos2,i)) / 2;
Ptab[id] += Ptab[(pos2 * taille) + i];
- Ptab[id] /= (T) 2;
+ Ptab[id] /= (long double) 2;
Ptab[jd] = Ptab[id];
}
}
@@ -1139,15 +1139,15 @@ template<class T> void Arbre::iNeighborJoining(Matrice<T> & distances) {
//_construction = 2;
}
-template<class T> void Arbre::iUPGMA(Matrice<T> & distances) {
+void Arbre::iUPGMA(Matrice & distances) {
reset();
Vecteur<int> etatMat;
- vector<T> accDistances;
+ vector<long double> accDistances;
Vecteur<ArbreNdBase *> tabPNoeuds;
long taille(distances.GetNL());
long i, j, pos1(0), pos2(0);
- T comparer;
+ long double comparer;
ArbreNdNoeud * Pnoeud(0);
if (distances.GetType() != 2) throw Anomalie(4);
@@ -1223,7 +1223,7 @@ template<class T> void Arbre::iUPGMA(Matrice<T> & distances) {
_oui_taille_branches = true;
}
-template<class T> void Arbre::iNeighborJoiningTopo(Matrice<T> & distances) {
+void Arbre::iNeighborJoiningTopo(Matrice & distances) {
reset();
//cerr << "Arbre::iNeighborJoiningTopo debut" << endl;
@@ -1232,10 +1232,10 @@ template<class T> void Arbre::iNeighborJoiningTopo(Matrice<T> & distances) {
long nblignemat;
long taille(distances.GetNL());
long i, j, pos1(0), pos2(0), pos3, id, jd, refi, refj;
- T comparer;
- T critere;
- T * Ptab(distances._tab);
- vector<T> accDistances;
+ long double comparer;
+ long double critere;
+ long double * Ptab(distances._tab);
+ vector<long double> accDistances;
ArbreNdNoeud * Pnoeud;
@@ -1315,7 +1315,7 @@ template<class T> void Arbre::iNeighborJoiningTopo(Matrice<T> & distances) {
for (i = 0; i < taille; i ++,id ++,jd += taille) {
if ((etatMat[i]) && (i != pos1)) {
Ptab[id] += Ptab[(pos2 * taille) + i];
- Ptab[id] /= (T) 2;
+ Ptab[id] /= (long double) 2;
Ptab[jd] = Ptab[id];
}
}
@@ -1550,7 +1550,7 @@ void Arbre::iDistances(MatriceLD & matrice) {
// f_tri_ind_alpha();
}
-void Arbre::iDistances(MatriceF & distances, int methode) {
+void Arbre::iDistances(MatriceLD & distances, int methode) {
//reconstruction d'arbres a partir d'une matrice de distances:
// int -> methode de reconstruction
// 1 -> UPGMA
@@ -1577,34 +1577,6 @@ void Arbre::iDistances(MatriceF & distances, int methode) {
// f_tri_ind_alpha();
}
-void Arbre::iDistances(MatriceLD & distances, int methode) {
-//reconstruction d'arbres a partir d'une matrice de distances:
- // int -> methode de reconstruction
- // 1 -> UPGMA
- // 2 -> Neighbor Joining
-//cerr << "Arbre::iDistances(MatriceLD & distances, int methode) debut" << endl;
- //on efface l'arbre si il yen a deja un
- reset();
-
-
- switch (methode) {
- case 1: // UPGMA
- iUPGMA(distances);
- break;
- case 101: // UPGMA
- iUPGMA(distances);
- break;
- case 2: // Neighbor Joining
- iNeighborJoining(distances);
- break;
- case 102: // Neighbor Joining, topologie seulement
- iNeighborJoiningTopo(distances);
- break;
- }
-//cerr << "Arbre::iDistances(MatriceLD & distances, int methode) tri" << endl;
-// f_tri_ind_alpha();
-}
-
void Arbre::f_forceiDistances(MatriceLD & distancesRef,int methodeArbre) {
bool continuer(true);
@@ -1642,7 +1614,7 @@ void Arbre::f_forceiDistances(MatriceLD & distancesRef,int methodeArbre) {
void Arbre::iNimbus(unsigned int nbessais , unsigned int nbind, unsigned int * Ptemp, char * * PPotu) {
unsigned int i, j;
ChaineCar nom;
- MatriceF tab_nimbus(nbind, nbessais) ;
+ MatriceLD tab_nimbus(nbind, nbessais) ;
unsigned int * Puint(Ptemp);
//cerr << "Arbre::iNimbus debut" << endl;
// Visu.reset((long unsigned int) nbind, (long unsigned int) nbessais);
@@ -1678,7 +1650,7 @@ void Arbre::iNimbus(unsigned int nbessais , unsigned int nbind, unsigned int * P
}
-void Arbre::iNimbusRec(ArbreNdNoeud * Pnoeud, MatriceF & tab_nimbus, unsigned int numessai, unsigned int deb, unsigned int fin, unsigned int longueur) {
+void Arbre::iNimbusRec(ArbreNdNoeud * Pnoeud, MatriceLD & tab_nimbus, unsigned int numessai, unsigned int deb, unsigned int fin, unsigned int longueur) {
// pos: position en nb d'essais
// branche regroupant les otus de 'deb' a 'fin'
unsigned int i, nbessais(tab_nimbus.GetNC());
diff --git a/src/arbre.h b/src/arbre.h
index 682a8b2..0ec50ef 100644
--- a/src/arbre.h
+++ b/src/arbre.h
@@ -221,7 +221,6 @@ public:
void iNimbus(unsigned int nbessais , unsigned int nbind, unsigned int * Ptemp, char * * PPotu);
void iDistances(MatriceLD &, int);
- void iDistances(MatriceF &, int);
void iDistances(MatriceLD & matrice);
void f_forceiDistances(MatriceLD & distancesRef,int methodeArbre);
@@ -252,9 +251,9 @@ protected:
ArbreNdNoeud * RechercheNoeud(const ArbreVectUINT &) const;
const ArbreNdOTU * RecherchePOTU(unsigned int id) const;
- template<class T> void iNeighborJoining(Matrice<T> & distances);
- template<class T> void iNeighborJoiningTopo(Matrice<T> & distances);
- template<class T> void iUPGMA(Matrice<T> & distances);
+ void iNeighborJoining(Matrice & distances);
+ void iNeighborJoiningTopo(Matrice & distances);
+ void iUPGMA(Matrice & distances);
float iPhylipRecGetTaille(istream & fichier);
float iPhylipRecGetForce(istream & fichier);
@@ -265,7 +264,7 @@ protected:
void oXML(ostream & fichier) const;
virtual void oPhylipEcritGroupes(ostream &) const {};
- void iNimbusRec(ArbreNdNoeud * Pnoeud, MatriceF & tab_nimbus, unsigned int numessai, unsigned int deb, unsigned int fin, unsigned int longueur=0);
+ void iNimbusRec(ArbreNdNoeud * Pnoeud, MatriceLD & tab_nimbus, unsigned int numessai, unsigned int deb, unsigned int fin, unsigned int longueur=0);
// void iPhylipRecPasser(istream & fichier);
void f_trishell_ind_alpha(unsigned int lb, unsigned int ub);
void f_tribulle_ind_alpha();// void f_tri_ind_alpha();
diff --git a/src/config.h b/src/config.h
index 29523ad..54c3595 100644
--- a/src/config.h
+++ b/src/config.h
@@ -1,7 +1,7 @@
#ifndef _CONFIG_H
#define _CONFIG_H
-#define POPULATIONS_VERSION "1.2.32"
+#define POPULATIONS_VERSION "1.2.33"
#include <QDebug>
diff --git a/src/matrices.cpp b/src/matrices.cpp
index 83a08dc..0c57e20 100644
--- a/src/matrices.cpp
+++ b/src/matrices.cpp
@@ -20,10 +20,8 @@
namespace biolib {
namespace vecteurs {
-//template<class T> int Matrice<T>::_oformat = 1; //Format de sortie: par d�faut
-
-template<class T> Matrice<T>::Matrice(const Matrice<T>& original) {
+Matrice::Matrice(const Matrice& original) {
//constructeur de copie
unsigned long i;
@@ -33,7 +31,7 @@ template<class T> Matrice<T>::Matrice(const Matrice<T>& original) {
_nl = original._nl;
_t = _nc * _nl;
- _tab = new T[_t];
+ _tab = new long double[_t];
_titre = original._titre;
_flag = original._flag;
@@ -49,7 +47,7 @@ template<class T> Matrice<T>::Matrice(const Matrice<T>& original) {
}
-template<class T> Matrice<T>::Matrice() {
+Matrice::Matrice() {
// _Pointeur = *( new (Pointeur<T>));
_oformat = 1;
@@ -62,14 +60,14 @@ template<class T> Matrice<T>::Matrice() {
_flag = 0;
}
-template<class T> Matrice<T>::Matrice(unsigned long nl, unsigned long nc) {
+Matrice::Matrice(unsigned long nl, unsigned long nc) {
unsigned long i;
_oformat = 1;
_nc = nc;
_nl = nl;
_t = nc * nl;
- _tab = new T[_t];
+ _tab = new long double[_t];
_type = 1;
_miss = 0;
@@ -88,7 +86,7 @@ template<class T> Matrice<T>::Matrice(unsigned long nl, unsigned long nc) {
}
-template<class T> bool Matrice<T>::SetType(int type) {
+bool Matrice::SetType(int type) {
switch (type) {
case 1: //rectangulaire normale
@@ -125,8 +123,8 @@ template<class T> bool Matrice<T>::SetType(int type) {
return (true);
}
-template<class T> const Matrice<T>& Matrice<T>::operator=(
- const Matrice<T> &rval) {
+const Matrice& Matrice::operator=(
+ const Matrice &rval) {
unsigned long i;
@@ -138,7 +136,7 @@ template<class T> const Matrice<T>& Matrice<T>::operator=(
_nc = rval._nc;
_nl = rval._nl;
_t = rval._t;
- _tab = new T[rval._t];
+ _tab = new long double[rval._t];
_titre = rval._titre;
@@ -151,7 +149,7 @@ template<class T> const Matrice<T>& Matrice<T>::operator=(
return (*this);
}
-template<class T> const Matrice<T>& Matrice<T>::operator=(vector<T> &rval) {
+const Matrice& Matrice::operator=(vector<long double> &rval) {
int i;
@@ -163,7 +161,7 @@ template<class T> const Matrice<T>& Matrice<T>::operator=(vector<T> &rval) {
_nc = rval.size();
_nl = 1;
_t = _nc;
- _tab = new T[_nc];
+ _tab = new long double[_nc];
// _titre = rval._titre;
@@ -176,7 +174,7 @@ template<class T> const Matrice<T>& Matrice<T>::operator=(vector<T> &rval) {
return (*this);
}
-template<class T> void Matrice<T>::oExcel(ostream& fichier) {
+void Matrice::oExcel(ostream& fichier) {
unsigned long i, j;
// fichier.setf(ios::scientific);
@@ -212,7 +210,7 @@ template<class T> void Matrice<T>::oExcel(ostream& fichier) {
}
-template<class T> void Matrice<T>::oGnumeric(ostream& fichier) {
+void Matrice::oGnumeric(ostream& fichier) {
QString * p_output_xml = new QString("");
QXmlStreamWriter xml_stream(p_output_xml);
xml_stream.setAutoFormatting(true);
@@ -340,7 +338,7 @@ template<class T> void Matrice<T>::oGnumeric(ostream& fichier) {
}
-template<class T> void Matrice<T>::oGnumericSheet(QXmlStreamWriter& xml_stream,
+void Matrice::oGnumericSheet(QXmlStreamWriter& xml_stream,
const QString & sheetname) const {
qDebug()
@@ -484,7 +482,7 @@ template<class T> void Matrice<T>::oGnumericSheet(QXmlStreamWriter& xml_stream,
}
-template<class T> void Matrice<T>::oNtsys(ostream& sortie) {
+void Matrice::oNtsys(ostream& sortie) {
unsigned long i, j, k, tmaxligne(100);
long pos;
@@ -582,11 +580,11 @@ template<class T> void Matrice<T>::oNtsys(ostream& sortie) {
}
}
-template<class T> T Matrice<T>::get_ppvaleur() const {
+long double Matrice::get_ppvaleur() const {
//retourne la plus petite valeur de la matrice
unsigned long taille(_nc * _nl);
unsigned long j;
- T ppvaleur(_tab[0]);
+ long double ppvaleur(_tab[0]);
for (j = 1; j < taille; j++)
if (_tab[j] < ppvaleur)
@@ -594,7 +592,7 @@ template<class T> T Matrice<T>::get_ppvaleur() const {
return (ppvaleur);
}
-template<class T> void Matrice<T>::f_neg2zero() {
+void Matrice::f_neg2zero() {
//remet � z�ro les chiffres n�gatifs
unsigned long taille(_nc * _nl);
unsigned long j(_nc * _nl);
@@ -604,10 +602,7 @@ template<class T> void Matrice<T>::f_neg2zero() {
_tab[j] = 0;
}
-template<class T> void Matrice<T>::iGnumeric(istream& entree) {
-}
-
-template<> void Matrice<long double>::iGnumeric(istream& entree) {
+void Matrice::iGnumeric(istream& entree) {
//lecture de matrices contenues dans les fichiers Gnumeric XML
#ifdef XmlParse_INCLUDED
//entree.seekg(0);
@@ -629,7 +624,7 @@ template<> void Matrice<long double>::iGnumeric(istream& entree) {
#endif
}
-template<class T> void Matrice<T>::iNtsys(istream& entree) {
+void Matrice::iNtsys(istream& entree) {
//lecture de matrices contenues dans les fichiers NTSYS
char car;
ChaineCar mot;
@@ -774,7 +769,7 @@ template<class T> void Matrice<T>::iNtsys(istream& entree) {
}
-template<class T> void Matrice<T>::iPhylip(istream& entree) {
+void Matrice::iPhylip(istream& entree) {
//lecture de matrices contenues dans des fichiers Phylip
ChaineCar mot;
ChaineCar sousmot;
@@ -852,7 +847,7 @@ template<class T> void Matrice<T>::iPhylip(istream& entree) {
}
-template<class T> void Matrice<T>::iExcel(istream& entree) {
+void Matrice::iExcel(istream& entree) {
//lecture de matrices contenues dans des fichiers Excel
// la matrice doit �tre indiqu�e par "/" ou "#" et commencer
// 1 case en dessous et � gauche.
@@ -990,7 +985,7 @@ template<class T> void Matrice<T>::iExcel(istream& entree) {
//}
}
-template<class T> void Matrice<T>::resize(unsigned long nblig,
+void Matrice::resize(unsigned long nblig,
unsigned long nbcol) {
unsigned long i;
@@ -1013,7 +1008,7 @@ template<class T> void Matrice<T>::resize(unsigned long nblig,
_nc = nbcol;
_nl = nblig;
_t = _nc * _nl;
- _tab = new T[_t];
+ _tab = new long double[_t];
// _miss = 0;
// _flag = 0;
@@ -1022,10 +1017,10 @@ template<class T> void Matrice<T>::resize(unsigned long nblig,
}
-template<class T> bool Matrice<T>::redim(unsigned long nblig,
+bool Matrice::redim(unsigned long nblig,
unsigned long nbcol) {
unsigned long i, j, t;
- T* Ptab;
+ long double* Ptab;
if (_tab == 0)
return (false);
@@ -1046,7 +1041,7 @@ template<class T> bool Matrice<T>::redim(unsigned long nblig,
Ptab = _tab;
t = nblig * nbcol;
- _tab = new T[t];
+ _tab = new long double[t];
for (i = 0; i < nblig; i++) {
for (j = 0; j < nbcol; j++) {
@@ -1064,7 +1059,7 @@ template<class T> bool Matrice<T>::redim(unsigned long nblig,
return (true);
}
-template<class T> void Matrice<T>::fslig(vector<long double>& somme) const {
+void Matrice::fslig(vector<long double>& somme) const {
int i, j;
@@ -1084,7 +1079,7 @@ template<class T> void Matrice<T>::fslig(vector<long double>& somme) const {
}
}
-template<class T> void Matrice<T>::fscol(vector<long double>& somme) const {
+void Matrice::fscol(vector<long double>& somme) const {
int pos, i, j;
@@ -1106,7 +1101,7 @@ template<class T> void Matrice<T>::fscol(vector<long double>& somme) const {
}
}
-template<class T> void Matrice<T>::ftranspose() {
+void Matrice::ftranspose() {
//transposition de matrices:
Titre swap;
@@ -1125,8 +1120,8 @@ template<class T> void Matrice<T>::ftranspose() {
else if (_flag == 2)
_flag = 1;
- T* Ptab;
- Ptab = new T[_t];
+ long double* Ptab;
+ Ptab = new long double[_t];
for (i = 0; i < _nl; i++) {
for (j = 0; j < _nc; j++) {
@@ -1142,10 +1137,10 @@ template<class T> void Matrice<T>::ftranspose() {
_tab = Ptab;
}
-template<class T> Matrice<T> Matrice<T>::operator*(Matrice<T> &rval) const {
+Matrice Matrice::operator*(Matrice &rval) const {
//produit matriciel
- Matrice<T> Resultat(_nl, rval._nc);
+ Matrice Resultat(_nl, rval._nc);
// long double limite(1e-030);
if (_nc != rval._nl)
@@ -1183,11 +1178,11 @@ template<class T> Matrice<T> Matrice<T>::operator*(Matrice<T> &rval) const {
return Resultat;
}
-template<class T> vector<T> Matrice<T>::operator*(const vector<T> &rval) {
+vector<long double> Matrice::operator*(const vector<long double> &rval) {
//produit d'une matrice par un vecteur
- vector<T> Resultat;
- Matrice<T>& lamatrice = *this;
+ vector<long double> Resultat;
+ Matrice& lamatrice = *this;
long i, k; //ligne, colonne
Resultat.resize(lamatrice._nl);
@@ -1206,9 +1201,9 @@ template<class T> vector<T> Matrice<T>::operator*(const vector<T> &rval) {
return Resultat;
}
-template<class T> Matrice<T> Matrice<T>::operator*(long double scalaire) {
+Matrice Matrice::operator*(long double scalaire) {
- Matrice<T> Resultat(_nl, _nc);
+ Matrice Resultat(_nl, _nc);
long i;
// Resultat.resize(_nl,_nc);
@@ -1232,9 +1227,9 @@ template<class T> Matrice<T> Matrice<T>::operator*(long double scalaire) {
return Resultat;
}
-template<class T> Matrice<T> Matrice<T>::operator-(Matrice<T>& rval) {
+Matrice Matrice::operator-(Matrice& rval) {
- Matrice<T> Resultat(_nl, _nc);
+ Matrice Resultat(_nl, _nc);
long i;
if (_nl != rval._nl)
@@ -1265,10 +1260,10 @@ template<class T> Matrice<T> Matrice<T>::operator-(Matrice<T>& rval) {
}
-template<class T> Matrice<T> Matrice<T>::operator+(Matrice<T> &rval) {
+Matrice Matrice::operator+(Matrice &rval) {
long i;
- Matrice<T> Resultat;
+ Matrice Resultat;
if (_nl != rval._nl)
throw Anomalie(4);
@@ -1299,7 +1294,7 @@ template<class T> Matrice<T> Matrice<T>::operator+(Matrice<T> &rval) {
}
-template<class T> long double Matrice<T>::fdet() const {
+long double Matrice::fdet() const {
//calcul du d�terminant d'une matrice par r�cursivit
// Olivier Langella 29 oct 98
// D'apr�s J. Lefebvre "introduction aux analyses statistiques
@@ -1308,7 +1303,7 @@ template<class T> long double Matrice<T>::fdet() const {
if (_nc != _nl)
throw Anomalie(4); //calcul impossible
- MatriceF calculs;
+ MatriceLD calculs;
calculs = *this;
@@ -1317,13 +1312,13 @@ template<class T> long double Matrice<T>::fdet() const {
return (det);
}
-template<class T> long double Matrice<T>::fdetrec() const {
+long double Matrice::fdetrec() const {
//calcul du d�terminant d'une matrice par r�cursivit
// utilis� par fdet;
long double det(0);
unsigned long i;
long cofacteur(1);
- Matrice<T> calculs;
+ Matrice calculs;
if (_nc == 2) {
//solution
@@ -1345,9 +1340,9 @@ template<class T> long double Matrice<T>::fdetrec() const {
}
}
-template<class T> void Matrice<T>::SupprCol(unsigned long nbcol) {
+void Matrice::SupprCol(unsigned long nbcol) {
unsigned long i, j, k, n;
- T * Ptab;
+ long double * Ptab;
// if (_nl > nblig) _tlig.erase(_tlig.begin() + _nl,_tlig.end());
if (nbcol < _tcol.size())
@@ -1355,7 +1350,7 @@ template<class T> void Matrice<T>::SupprCol(unsigned long nbcol) {
n = _nc - 1;
- Ptab = new T[n * _nl];
+ Ptab = new long double[n * _nl];
k = 0;
for (i = 0; i < _nl; i++) {
@@ -1377,9 +1372,9 @@ template<class T> void Matrice<T>::SupprCol(unsigned long nbcol) {
}
-template<class T> void Matrice<T>::SupprLig(unsigned long nblig) {
+void Matrice::SupprLig(unsigned long nblig) {
unsigned long i, j, k, n;
- T* Ptab;
+ long double* Ptab;
// if (_nl > nblig) _tlig.erase(_tlig.begin() + _nl,_tlig.end());
if (nblig < _tlig.size())
@@ -1387,7 +1382,7 @@ template<class T> void Matrice<T>::SupprLig(unsigned long nblig) {
n = _nl - 1;
- Ptab = new T[n * _nc];
+ Ptab = new long double[n * _nc];
k = 0;
for (i = 0; i < _nl; i++) {
@@ -1409,7 +1404,7 @@ template<class T> void Matrice<T>::SupprLig(unsigned long nblig) {
}
-void MatriceF::finv(MatriceF& inverse) const {
+void MatriceLD::finv(MatriceLD& inverse) const {
//calcul de l'inverse d'une matrice
// Olivier Langella 29 oct 98
// D'apr�s J. Lefebvre "introduction aux analyses statistiques
@@ -1418,7 +1413,7 @@ void MatriceF::finv(MatriceF& inverse) const {
throw Anomalie(4); //calcul impossible
long double detA;
- MatriceF calculs;
+ MatriceLD calculs;
int cofacteur, cofl(-1);
unsigned long i, j;
@@ -1442,7 +1437,7 @@ void MatriceF::finv(MatriceF& inverse) const {
}
-void MatriceF::fvalpropres(Matrice<float>& vectpropres,
+void MatriceLD::fvalpropres(MatriceLD& vectpropres,
vector<float>& valpropres, float precision) {
//Calcul des valeurs propres pour une matrice sym�trique
@@ -1459,8 +1454,8 @@ void MatriceF::fvalpropres(Matrice<float>& vectpropres,
valpropres.resize(_nc);
vectpropres.resize(_nc, _nc);
vectpropres.SetType(1);
- MatriceF matC;
- MatriceF matA;
+ MatriceLD matC;
+ MatriceLD matA;
matA = *this;
matA._titre.push_back("Matrice A");
@@ -1480,7 +1475,7 @@ void MatriceF::fvalpropres(Matrice<float>& vectpropres,
}
matC.resize(nc, nc);
- MatriceF matInter(nc, nc); //matrice pour les calculs
+ MatriceLD matInter(nc, nc); //matrice pour les calculs
//intermediaires
do {
// choix du point � annuler
@@ -1548,7 +1543,7 @@ void MatriceF::fvalpropres(Matrice<float>& vectpropres,
}
-template<class T> long double Matrice<T>::ftrace() const {
+long double Matrice::ftrace() const {
//calcul de la trace d'une matrice (somme des E diagonaux)
// Olivier Langella 29 oct 98
if (_nc != _nl)
@@ -1566,9 +1561,9 @@ template<class T> long double Matrice<T>::ftrace() const {
return res;
}
-template<class T> Matrice<T> Matrice<T>::operator+(long double rval) {
+Matrice Matrice::operator+(long double rval) {
- Matrice<T> Resultat;
+ Matrice Resultat;
Resultat = *this;
unsigned long i;
@@ -1581,8 +1576,8 @@ template<class T> Matrice<T> Matrice<T>::operator+(long double rval) {
}
-template<class T> void Matrice<T>::fswapcol(long i, long j) {
- T swap;
+void Matrice::fswapcol(long i, long j) {
+ long double swap;
long k;
for (k = 0; k < _nc; k++) {
@@ -1592,12 +1587,12 @@ template<class T> void Matrice<T>::fswapcol(long i, long j) {
}
}
-template<class T> void Matrice<T>::fmultiplier(const Matrice<T>& matA,
- const Matrice<T>& matB) {
+void Matrice::fmultiplier(const Matrice& matA,
+ const Matrice& matB) {
//pour multiplier 2 matrices plus rapidement
// A et B sont carrees !!!!
long i, j, k, nc(_nc);
- T res;
+ long double res;
for (i = 0; i < nc; i++) {
for (j = 0; j < nc; j++) {
@@ -1610,7 +1605,7 @@ template<class T> void Matrice<T>::fmultiplier(const Matrice<T>& matA,
}
}
-template<class T> void Matrice<T>::oXgobi(const string &fnom) {
+void Matrice::oXgobi(const string &fnom) {
unsigned long i, j;
ofstream fichier;
// string fnom(nomfichier);
@@ -1680,7 +1675,7 @@ template<class T> void Matrice<T>::oXgobi(const string &fnom) {
////////////////////////////////////////////////
// GLOBAL
///////////////////////////////////////////////
-template<class T> ostream& operator<<(ostream& sortie, Matrice<T>& lamatrice) {
+ostream& operator<<(ostream& sortie, Matrice& lamatrice) {
//1= Excel
//2= Ntsys
//3= xgobi ==!!!! seulement en ofstream !!!!!
@@ -1690,7 +1685,7 @@ template<class T> ostream& operator<<(ostream& sortie, Matrice<T>& lamatrice) {
}
-template<class T> ofstream& operator<<(ofstream& sortie, Matrice<T>& lamatrice) {
+ofstream& operator<<(ofstream& sortie, Matrice& lamatrice) {
//1= Excel
//2= Ntsys
//3= xgobi ==!!!! seulement en ofstream !!!!!
@@ -1719,7 +1714,7 @@ template<class T> ofstream& operator<<(ofstream& sortie, Matrice<T>& lamatrice)
}*/
-template<class T> istream& operator>>(istream& ientree, Matrice<T>& lamatrice) {
+istream& operator>>(istream& ientree, Matrice& lamatrice) {
//cerr << "coucou";
lamatrice.iFichier(ientree);
@@ -1727,7 +1722,7 @@ template<class T> istream& operator>>(istream& ientree, Matrice<T>& lamatrice) {
return (ientree);
}
-template<class T> void Matrice<T>::oPhylip(ostream& fichier) {
+void Matrice::oPhylip(ostream& fichier) {
unsigned long i, j;
fichier.setf(ios::scientific);
@@ -1767,7 +1762,7 @@ template<class T> void Matrice<T>::oPhylip(ostream& fichier) {
}
-template<class T> void Matrice<T>::iFichier(istream& ientree) {
+void Matrice::iFichier(istream& ientree) {
int nbformat(6), i(1);
char car;
bool autre(true);
@@ -1819,7 +1814,7 @@ template<class T> void Matrice<T>::iFichier(istream& ientree) {
}
MatriceLD::MatriceLD() :
- Matrice<long double> () {
+ Matrice () {
}
;
diff --git a/src/matrices.h b/src/matrices.h
index e571fe3..1a7b804 100644
--- a/src/matrices.h
+++ b/src/matrices.h
@@ -47,9 +47,8 @@ namespace biolib {
namespace vecteurs {
class MatriceLD;
-class MatriceF;
// les matrices
-template<class T> class Matrice {
+class Matrice {
public:
Matrice();
Matrice(unsigned long nl, unsigned long nc = 0);
@@ -61,7 +60,7 @@ public:
delete[] _tab;
}
- virtual T& GetCase(const ChaineCar& nomLig, const ChaineCar& nomCol) const {
+ virtual long double& GetCase(const ChaineCar& nomLig, const ChaineCar& nomCol) const {
long ni(_tlig.Position(nomLig));
long nj(_tcol.Position(nomCol));
//cerr << nomLig << "GetCase ni " << ni;
@@ -71,7 +70,7 @@ public:
return (GetCase(ni, nj));
}
- virtual T& GetCase(unsigned long i, unsigned long j) const {
+ virtual long double& GetCase(unsigned long i, unsigned long j) const {
if ((i >= _nl) || (j >= _nc))
throw Anomalie(7);
//renvoie la valeur de la case i (ligne), j (colonne)
@@ -106,7 +105,7 @@ public:
return (_flag);
}
- virtual T get_ppvaleur() const; //recherche la plus petite valeur
+ virtual long double get_ppvaleur() const; //recherche la plus petite valeur
virtual bool SetType(int type); //type de matrice:
//1 -> rectangulaire
@@ -124,7 +123,7 @@ public:
long double fdet() const;
long double ftrace() const;
- inline void fmultiplier(const Matrice<T>& matA, const Matrice<T>& matB);
+ inline void fmultiplier(const Matrice& matA, const Matrice& matB);
Titre _titre;
@@ -217,14 +216,14 @@ public:
void oPhylip(ostream& sortie);
void oXgobi(const string&);
- virtual const Matrice<T>& operator=(const Matrice<T> &rval);
- const Matrice<T>& operator=(vector<T> &rval);
- Matrice<T> operator*(Matrice<T> &rval) const;
- vector<T> operator*(const vector<T> &rval);
- Matrice<T> operator*(long double scalaire);
- Matrice<T> operator-(Matrice<T> &rval);
- Matrice<T> operator+(Matrice<T> &rval);
- Matrice<T> operator+(long double rval);
+ virtual const Matrice& operator=(const Matrice &rval);
+ const Matrice& operator=(vector<long double> &rval);
+ Matrice operator*(Matrice &rval) const;
+ vector<long double> operator*(const vector<long double> &rval);
+ Matrice operator*(long double scalaire);
+ Matrice operator-(Matrice &rval);
+ Matrice operator+(Matrice &rval);
+ Matrice operator+(long double rval);
protected:
@@ -246,7 +245,7 @@ protected:
public:
- T* _tab; // matrice
+ long double* _tab; // matrice
//formats de fichiers
unsigned int _oformat; //1-> Excel 2->NTsys 3->xgobi (UNIX) 4->phylip
@@ -301,49 +300,20 @@ public:
};
-class MatriceF: public Matrice<float> {
-
-public:
- MatriceF() :
- Matrice<float> () {
- }
-
- MatriceF(unsigned long nl, unsigned long nc = 0) :
- Matrice<float> (nl, nc) {
- }
-
- MatriceF(const MatriceF& lamatrice) :
- Matrice<float> (lamatrice) {
- }
- //constructeur de copie
- MatriceF(const Matrice<float>& lamatrice) :
- Matrice<float> (lamatrice) {
- }
- //constructeur de copie
- ~MatriceF() {
- }
-
- void finv(MatriceF& resultat) const;
-
- void fvalpropres(Matrice<float>&, vector<float> &, float precision =
- 0.000001);
-
-};
-
// les matrices
-class MatriceLD: public Matrice<long double> {
+class MatriceLD: public Matrice {
public:
MatriceLD();
MatriceLD(long nl, long nc = 0) :
- Matrice<long double> (nl, nc) {
+ Matrice (nl, nc) {
}
MatriceLD(const MatriceLD& lamatrice) :
- Matrice<long double> (lamatrice) {
+ Matrice (lamatrice) {
}
//constructeur de copie
- MatriceLD(const Matrice<long double>& lamatrice) :
- Matrice<long double> (lamatrice) {
+ MatriceLD(const Matrice& lamatrice) :
+ Matrice (lamatrice) {
}
//constructeur de copie
virtual ~MatriceLD() {
@@ -372,6 +342,12 @@ public:
void fvalpropres (MatriceLD&, vector<long double> &, long double precision=0.000001);
*/
+
+ void finv(MatriceLD& resultat) const;
+
+ void fvalpropres(MatriceLD&, vector<float> &, float precision =
+ 0.000001);
+
};
// les tableaux de matrices
@@ -453,13 +429,13 @@ public:
};
-template<class T> ostream& operator<<(ostream& sortie, Matrice<T>& lamatrice);
+ostream& operator<<(ostream& sortie, Matrice& lamatrice);
//ofstream& operator<<(ofstream& sortie,MatriceLD& lamatrice);
-template<class T> ofstream& operator<<(ofstream& sortie, Matrice<T>& lamatrice);
+ofstream& operator<<(ofstream& sortie, Matrice& lamatrice);
-template<class T> istringstream& operator>>(istringstream& ientree,
- Matrice<T>& lamatrice);
+istringstream& operator>>(istringstream& ientree,
+ Matrice& lamatrice);
} //namespace biolib {
} //namespace vecteurs {
diff --git a/src/populations b/src/populations
index c59dff5..da2aace 100755
Binary files a/src/populations and b/src/populations differ
diff --git a/test.svg b/test.svg
new file mode 100644
index 0000000..5509d46
--- /dev/null
+++ b/test.svg
@@ -0,0 +1,220 @@
+<?xml version="1.0" encoding="ISO-8859-1" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
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+<title>SVG drawing</title>
+<desc>This was produced by version 4.2 of GNU libplot, a free library for exporting 2-D vector graphics.</desc>
+<rect id="background" x="0" y="0" width="1" height="1" stroke="none" fill="white"/>
+<g id="content" transform="translate(0,1) scale(1,-1) scale(0.00033333) " xml:space="preserve" stroke="black" stroke-linecap="butt" stroke-linejoin="miter" stroke-miterlimit="10.433" stroke-dasharray="none" stroke-dashoffset="0" stroke-opacity="1" fill="none" fill-rule="even-odd" fill-opacity="1" font-style="normal" font-variant="normal" font-weight="normal" font-stretch="normal" font-size-adjust="none" letter-spacing="normal" word-spacing="normal" text-anchor="start">
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diff --git a/test.tre b/test.tre
new file mode 100644
index 0000000..1cd993b
--- /dev/null
+++ b/test.tre
@@ -0,0 +1,2 @@
+[Neighbor-Joining]
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--
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