[med-svn] [physamp] 01/02: Imported Upstream version 0.2.0
Andreas Tille
tille at debian.org
Sat Aug 13 06:13:44 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository physamp.
commit 4c0161bb3d0d399a41c02075f3d7cccc633c3fe7
Author: Andreas Tille <tille at debian.org>
Date: Sat Aug 13 08:12:38 2016 +0200
Imported Upstream version 0.2.0
---
AUTHORS.txt | 1 +
CMakeLists.txt | 268 +
COPYING.txt | 675 +
ChangeLog | 5 +
INSTALL.txt | 12 +
doc/CMakeLists.txt | 7 +
doc/physamp.texi | 226 +
examples/PF01049/AlnOptimAuto.bpp | 23 +
examples/PF01049/AlnOptimFasttree.bpp | 24 +
examples/PF01049/AlnOptimFasttreeStop.bpp | 24 +
examples/PF01049/PF01049_fasttree.dnd | 1 +
examples/PF01049/PF01049_full.txt | 19824 ++++++++++++++++++++++++++++
examples/PF01049/README | 12 +
examples/PF01049/diagnostic.R | 60 +
man/CMakeLists.txt | 7 +
man/bppalnoptim.1.txt | 37 +
physamp/AlignmentOptimizer.cpp | 775 ++
physamp/CMakeLists.txt | 17 +
18 files changed, 21998 insertions(+)
diff --git a/AUTHORS.txt b/AUTHORS.txt
new file mode 100644
index 0000000..34cfb4a
--- /dev/null
+++ b/AUTHORS.txt
@@ -0,0 +1 @@
+Julien Dutheil <julien.dutheil at univ-montp2.fr>
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 0000000..4a3446e
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,268 @@
+# CMake script for the physamp package
+# Author: Julien Dutheil
+# Created: 24/10/2014
+
+# Global parameters
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+PROJECT(physamp CXX)
+
+IF(NOT CMAKE_BUILD_TYPE)
+ SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
+ "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
+ FORCE)
+ENDIF()
+
+SET(CMAKE_CXX_FLAGS "-Wall -Weffc++ -Wshadow -Wconversion")
+
+IF(NOT NO_DEP_CHECK)
+ SET(NO_DEP_CHECK FALSE CACHE BOOL
+ "Disable dependencies check for building distribution only."
+ FORCE)
+ENDIF(NOT NO_DEP_CHECK)
+
+IF(NOT DOC_COMPRESS)
+ SET(DOC_COMPRESS gzip CACHE STRING
+ "Set program for compressing documentation."
+ FORCE)
+ENDIF(NOT DOC_COMPRESS)
+
+IF(NOT DOC_COMPRESS_EXT)
+ SET(DOC_COMPRESS_EXT gz CACHE STRING
+ "Set extension of compressed documentation."
+ FORCE)
+ENDIF(NOT DOC_COMPRESS_EXT)
+
+
+IF(NO_DEP_CHECK)
+ MESSAGE("-- Dependencies checking disabled. Only distribution can be built.")
+ELSE(NO_DEP_CHECK)
+
+
+#static linkage?
+IF(NOT BUILD_STATIC)
+ SET(BUILD_STATIC FALSE CACHE BOOL
+ "Enable static linkage."
+ FORCE)
+ENDIF()
+IF(BUILD_STATIC)
+ MESSAGE("-- Static linkage requested.")
+ SET(CMAKE_CXX_FLAGS "-static -static-libgcc ${CMAKE_CXX_FLAGS}")
+ENDIF()
+
+#build info?
+IF(NOT DEFINED INFO)
+ SET(INFO UNIX)
+ENDIF(NOT DEFINED INFO)
+
+#build man pages?
+IF(NOT DEFINED MAN)
+ SET(MAN UNIX)
+ENDIF(NOT DEFINED MAN)
+
+#find executables for documentation
+IF(MAN)
+ FIND_PROGRAM(NROFF_EXE NAMES nroff)
+ IF(NROFF_EXE)
+ MESSAGE("-- Found nroff here: ${NROFF_EXE}")
+ MESSAGE(" Adding targets: man")
+
+ ADD_CUSTOM_TARGET(man
+ ALL
+ #COMMAND cp bppphysamp.1.txt bppphysamp.1
+ #COMMAND ${DOC_COMPRESS} -f bppphysamp.1
+ COMMAND cp bppalnoptim.1.txt bppalnoptim.1
+ COMMAND ${DOC_COMPRESS} -f bppalnoptim.1
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/man
+ )
+ SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "man/bppalnoptim.1.${DOC_COMPRESS_EXT};man/bppphysamp.1.${DOC_COMPRESS_EXT};")
+
+ ELSE()
+ MESSAGE(FATAL_ERROR "Program nroff required but not found.")
+ ENDIF()
+ENDIF(MAN)
+
+IF(INFO)
+ FIND_PROGRAM(MAKEINFO_EXE NAMES makeinfo)
+ IF(MAKEINFO_EXE)
+ MESSAGE("-- Found makeinfo here: ${MAKEINFO_EXE}")
+ MESSAGE(" Adding targets: info, html")
+
+ SET(ADD_INFO_TO "ALL")
+ MESSAGE(" Adding target info to target all")
+
+ ADD_CUSTOM_TARGET(info
+ ${ADD_INFO_TO}
+ COMMAND ${MAKEINFO_EXE} physamp.texi
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/doc
+ )
+
+ ADD_CUSTOM_TARGET(html
+ COMMAND ${MAKEINFO_EXE} --html --css-ref=http://www.w3.org/StyleSheets/Core/Steely physamp.texi
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/doc
+ )
+ ELSE(MAKEINFO_EXE)
+ MESSAGE(FATAL_ERROR p"Program makeinfo required but not found.")
+ ENDIF(MAKEINFO_EXE)
+ENDIF(INFO)
+
+FIND_PROGRAM(PDFTEX_EXE NAMES pdftex)
+IF(PDFTEX_EXE)
+ MESSAGE("-- Found pdftex here: ${PDFTEX_EXE}")
+ MESSAGE(" Adding target: pdf")
+
+ ADD_CUSTOM_TARGET(pdf
+ COMMAND ${PDFTEX_EXE} physamp.texi
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/doc
+ )
+ SET_DIRECTORY_PROPERTIES(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "doc/physamp.pdf;doc/physamp.aux;doc/physamp.cp;doc/physamp.fn;doc/physamp.info;doc/physamp.ky;doc/physamp.log;doc/physamp.pg;doc/physamp.toc;doc/physamp.tp;doc/physamp.vr")
+ENDIF(PDFTEX_EXE)
+
+#here is a useful function:
+MACRO(IMPROVED_FIND_LIBRARY OUTPUT_LIBS lib_name include_to_find)
+ #start:
+ FIND_PATH(${lib_name}_INCLUDE_DIR ${include_to_find})
+ INCLUDE_DIRECTORIES(${${lib_name}_INCLUDE_DIR})
+
+ IF(BUILD_STATIC)
+ SET(${lib_name}_STATIC_NAMES lib${lib_name}.a)
+ FIND_LIBRARY(${lib_name}_STATIC_LIBRARY NAMES ${${lib_name}_STATIC_NAMES} PATH_SUFFIXES lib${LIB_SUFFIX})
+ IF(${lib_name}_STATIC_LIBRARY)
+ MESSAGE("-- Library ${lib_name} found here:")
+ MESSAGE(" includes: ${${lib_name}_INCLUDE_DIR}")
+ MESSAGE(" static libraries: ${${lib_name}_STATIC_LIBRARY}")
+ ELSE()
+ MESSAGE(FATAL_ERROR "${lib_name} required but not found.")
+ ENDIF()
+ #add the dependency:
+ SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_STATIC_LIBRARY})
+ ELSE()
+ SET(${lib_name}_NAMES ${lib_name} ${lib_name}.lib ${lib_name}.dll)
+ FIND_LIBRARY(${lib_name}_LIBRARY NAMES ${${lib_name}_NAMES} PATH_SUFFIXES lib${LIB_SUFFIX})
+ IF(${lib_name}_LIBRARY)
+ MESSAGE("-- Library ${lib_name} found here:")
+ MESSAGE(" includes: ${${lib_name}_INCLUDE_DIR}")
+ MESSAGE(" dynamic libraries: ${${lib_name}_LIBRARY}")
+ ELSE()
+ MESSAGE(FATAL_ERROR "${lib_name} required but not found.")
+ ENDIF()
+ #add the dependency:
+ SET(${OUTPUT_LIBS} ${${OUTPUT_LIBS}} ${${lib_name}_LIBRARY})
+ ENDIF()
+
+ENDMACRO(IMPROVED_FIND_LIBRARY)
+
+# Set the CMAKE_PREFIX_PATH for the find_library fonction when using non
+# standard install location
+IF(CMAKE_INSTALL_PREFIX)
+ SET(CMAKE_PREFIX_PATH "${CMAKE_INSTALL_PREFIX}" ${CMAKE_PREFIX_PATH})
+ENDIF(CMAKE_INSTALL_PREFIX)
+
+#Find the libraries. The order is very important for static linkage, it won't
+#link if you change it!
+IMPROVED_FIND_LIBRARY(LIBS bpp-phyl Bpp/Phyl/Tree.h)
+IMPROVED_FIND_LIBRARY(LIBS bpp-seq Bpp/Seq/Alphabet/Alphabet.h)
+IMPROVED_FIND_LIBRARY(LIBS bpp-core Bpp/Clonable.h)
+
+# Subdirectories
+ADD_SUBDIRECTORY(physamp)
+ADD_SUBDIRECTORY(doc)
+ADD_SUBDIRECTORY(man)
+
+ENDIF(NO_DEP_CHECK)
+
+# Packager
+SET(CPACK_PACKAGE_NAME "physamp")
+SET(CPACK_PACKAGE_VENDOR "Julien Y. Dutheil")
+SET(CPACK_PACKAGE_VERSION "0.2.0")
+SET(CPACK_PACKAGE_VERSION_MAJOR "0")
+SET(CPACK_PACKAGE_VERSION_MINOR "2")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Phylogenetic Sampler package")
+SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
+SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")
+SET(CPACK_RESOURCE_FILE_INSTALL "${CMAKE_SOURCE_DIR}/INSTALL.txt")
+SET(CPACK_SOURCE_GENERATOR "TGZ")
+SET(CPACK_SOURCE_IGNORE_FILES
+ "CMakeFiles"
+ "Makefile"
+ "_CPack_Packages"
+ "CMakeCache.txt"
+ ".*\\\\.cmake"
+ ".*\\\\.git"
+ ".*\\\\.gz"
+ ".*\\\\.zip"
+ ".*\\\\.deb"
+ ".*\\\\.rpm"
+ ".*\\\\.dmg"
+ ".*\\\\.sh"
+ ".*\\\\..*\\\\.swp"
+ ".*stamp"
+ "\\\\.sh"
+ "bppSuite/\\\\..*"
+ "bppSuite/bppphysamp"
+ "bppSuite/bppalnoptim"
+ "doc/physamp/"
+ "doc/physamp\\\\.info"
+ "doc/physamp\\\\.toc"
+ "doc/physamp\\\\.vr"
+ "doc/physamp\\\\.tp"
+ "doc/physamp\\\\.log"
+ "doc/physamp\\\\.fn"
+ "doc/physamp\\\\.ky"
+ "doc/physamp\\\\.cp"
+ "doc/physamp\\\\.pg"
+ "doc/physamp\\\\.aux"
+ "doc/physamp\\\\.pdf"
+ "man/.*\\\\.1.${DOC_COMPRESS_EXT}"
+ "debian/tmp"
+ "debian/physamp/"
+ "debian/physamp\\\\.substvars"
+ "debian/physamp\\\\.debhelper"
+ "debian/debhelper\\\\.log"
+ "install_manifest.txt"
+ "DartConfiguration.tcl"
+ ${CPACK_SOURCE_IGNORE_FILES}
+)
+IF (MACOS)
+ SET(CPACK_GENERATOR "Bundle")
+ENDIF()
+
+SET(CPACK_SOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}")
+SET(CPACK_DEBSOURCE_PACKAGE_FILE_NAME "${CMAKE_PROJECT_NAME}_${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}.orig")
+INCLUDE(CPack)
+
+#This adds the 'dist' target
+ADD_CUSTOM_TARGET(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
+# 'clean' is not (yet) a first class target. However, we need to clean the directories before building the sources:
+IF("${CMAKE_GENERATOR}" MATCHES "Make")
+ ADD_CUSTOM_TARGET(make_clean
+ COMMAND ${CMAKE_MAKE_PROGRAM} clean
+ WORKING_DIRECTORY ${CMAKE_CURRENT_DIR}
+ )
+ ADD_DEPENDENCIES(dist make_clean)
+
+ ADD_CUSTOM_TARGET(make_clean_man
+ COMMAND rm -f *.${DOC_COMPRESS_EXT}
+ WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}/man
+ )
+ ADD_DEPENDENCIES(dist make_clean_man)
+ENDIF()
+
+IF(NOT NO_DEP_CHECK)
+IF (UNIX)
+#This creates deb packages:
+ADD_CUSTOM_TARGET(origdist COMMAND cp ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz ../${CPACK_DEBSOURCE_PACKAGE_FILE_NAME}.tar.gz)
+ADD_DEPENDENCIES(origdist dist)
+ADD_CUSTOM_TARGET(deb dpkg-buildpackage -uc -us -i${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
+ADD_DEPENDENCIES(deb origdist)
+ADD_DEPENDENCIES(deb info man)
+
+#This creates rpm packages:
+ADD_CUSTOM_TARGET(rpm rpmbuild -ta ${CPACK_SOURCE_PACKAGE_FILE_NAME}.tar.gz)
+ADD_DEPENDENCIES(rpm dist info man)
+
+#ADD_DEPENDENCIES(info install)
+
+ENDIF(UNIX)
+
+ENDIF(NOT NO_DEP_CHECK)
diff --git a/COPYING.txt b/COPYING.txt
new file mode 100644
index 0000000..3ad63e0
--- /dev/null
+++ b/COPYING.txt
@@ -0,0 +1,675 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ 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.
+
+ Preamble
+
+ The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+ The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works. By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users. We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors. You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
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diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..b371117
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,5 @@
+30/03/15 -*- Version 0.2.0 -*-
+
+30/03/15 Julien Dutheil
+* New entropy calculation
+* Faster overlap distance calculation
diff --git a/INSTALL.txt b/INSTALL.txt
new file mode 100644
index 0000000..c8859da
--- /dev/null
+++ b/INSTALL.txt
@@ -0,0 +1,12 @@
+This software needs cmake >= 2.6 to build.
+
+After installing cmake, run it with the following command:
+cmake -DCMAKE_INSTALL_PREFIX=[where to install, for instance /usr/local or $HOME/.local] .
+
+If available, you can also use ccmake instead of cmake for a more user-friendly interface.
+
+Then compile and install the software with
+make install
+
+You may also consider installing and using the software checkinstall for easier system administration.
+
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
new file mode 100644
index 0000000..b89ac1a
--- /dev/null
+++ b/doc/CMakeLists.txt
@@ -0,0 +1,7 @@
+# CMake script for the physamp package
+# Author: Julien Dutheil
+# Created: 24/10/2014
+
+IF(INFO)
+ INSTALL(FILES physamp.info DESTINATION share/info)
+ENDIF(INFO)
diff --git a/doc/physamp.texi b/doc/physamp.texi
new file mode 100644
index 0000000..b29b651
--- /dev/null
+++ b/doc/physamp.texi
@@ -0,0 +1,226 @@
+\input texinfo @c -*-texinfo-*-
+ at c %**start of header
+ at setfilename physamp.info
+ at settitle PhySamp Manual 0.2.0
+ at documentencoding UTF-8
+ at afourpaper
+ at dircategory Science Biology Genetics
+ at direntry
+* bppalnoptim: (bppalnoptim) Alignment Optimizer.
+ at end direntry
+ at c %**end of header
+
+
+ at copying
+This is the manual of the PhySamp package, version 0.2.0.
+
+Copyright @copyright{} 2015 Julien Y. Dutheil
+ at end copying
+
+ at titlepage
+ at title PhySamp Manual
+ at author Julien Dutheil
+ at author @email{dutheil@@evolbio.mpg.de}
+
+ at c The following two commands start the copyright page.
+ at page
+ at vskip 0pt plus 1fill1
+ at insertcopying
+ at end titlepage
+
+ at c Output the table of contents at the beginning.
+ at contents
+
+ at ifnottex
+ at node Top, Introduction, (dir), (dir)
+ at top The PhySamp Manual
+
+ at insertcopying
+ at end ifnottex
+
+ at menu
+* Introduction::
+* bppalnoptim::
+
+ at detailmenu
+ --- The Detailed Node Listing ---
+
+Introduction
+
+* Description::
+* Run::
+
+ at end detailmenu
+ at end menu
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at node Introduction, bppalnoptim, Top, Top
+ at chapter Introduction
+
+PhySamp is a software package for phylogenetic sampling. Its aim is to optimize a sequence alignment data set based on its corresponding phylogeny.
+
+PhySamp is written on the Bio++ libraries, and uses the BppO syntax for options, introduced with the Bio++ Program Suite software (BppSuite). Part of this manual will therefore link to the corresponding manual of BppSuite where needed, and only describe options specific to the PhySamp package.
+
+Note that several detailed examples are provided along with the source code of the program, and can serve as good training starts. This manual intends to provide an exhaustive description of the options used in these examples.
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at menu
+* Description::
+* Run::
+ at end menu
+
+ at node Description, Run, Introduction, Introduction
+ at section Description of the programs
+
+The PhySamp package currently contains one program:
+
+ at table @samp
+
+ at item bppalnoptim
+optimize a sequence alignment by removing sequences in order to maximize the number of sites with a minimal coverage.
+
+ at end table
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at node Run, , Description, Introduction
+ at section How to run the program
+
+Programs in the PhySamp package follow the @samp{BppO} syntax. They are command line driven, and take as input options with the format @samp{name}=@samp{value}. These options can be gathered into a file, and loaded using @command{param=optionfile}. Please refer to the Bio++ Program Suite manual for more details, including the use of variables, priority of option values, etc.
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at node bppalnoptim, , Introduction, Top
+ at chapter Sampling alignment to maximize the number of sites with minimum coverage
+
+The option files for @sc{bppalnoptim} fall in three sections: input of alignment and guide tree, filter parameters and output files.
+
+ at section Input files
+
+ at sc{bppalnoptim} reads a sequence alignment file using the same syntax as all bppSuite programs (@ref{Sequences, , , bppsuite, @uref{http://biopp.univ-montp2.fr/manual/html/bppsuite/2.2.0/Sequences.html#Sequences}}). All formats are supported, as well as sequence filtering options.
+
+In order to perform its sampling procedure, @sc{bppalnoptim} requires a @emph{guide tree}. This guide tree can be provided as input or built using a sequence hierarchical clustering approach.
+Providing a guide tree will be in most cases faster, as software like FastTree can produce accurate phylogenetic trees for large data sets in a very short time.
+
+ at itemize @bullet
+ at item
+User-defined guide tree are provided using the option @command{input.tree.method=File}, and the standard option for reading tree files in the BppO syntax (@ref{Sequences, , , bppsuite, @uref{http://biopp.univ-montp2.fr/manual/html/bppsuite/2.2.0/Tree.html#Tree}}).
+ at item
+Clustering trees are built using the option @command{input.tree.method = AutoCluster(linkage=@{linkage_mode@})}, where @command{@{linkage_mode@}} is one of @emph{single}, @emph{complete}, @emph{median}, @emph{average}, @emph{centroid} or @emph{ward}.
+ at end itemize
+
+ at section Sampling mode and parameters
+
+A few option enables the configuration of the sampling procedure:
+ at table @command
+ at item filter_gaps = @{yes/no@}
+Tell if gap characters ('-') should be considered as missing data.
+ at item filter_unresolved = @{yes/no@}
+Tell if unresolved characters such as 'N' (nucleotides) and 'X' (proteins) should be considered as missing data.
+ at item threshold = @{float[0,1]@}
+The minimum coverage for a site to be included in the analysis. A threshold of 0.7 means that only sites with no more than 30\% gaps (or unresolved characters, if @command{filter_unresolved=yes}) will be considered suitable.
+ at item method = @{Diagnostic|Input|Auto@}
+One of three possible running modes, which are detailed below.
+ at item comparison = @{MaxSites|MaxChars@}
+Criterion to compare sequences subsets. @command{MaxSites} will maximize the number of sites with minimal coverage (default), while @command{MaxChars} will maximize the amount of data (number of sequences * number of sites).
+ at end table
+
+Here comes a description of the three running modes:
+
+ at subsection Running mode: Input
+
+This is an interactive mode, where the user is prompt for which sequence to select at each iteration:
+ at example
+ at group
+Number of sequences in alignment.......: 1652
+Number of sites in alignment...........: 129
+Number of chars in alignment...........: 182603
+Choice Node #seq %seq #sites %sites #chars %chars
+1) 2030 1647 -5 131 +2 184714 2111
+2) 404 1647 -5 131 +2 184636 2033
+3) 1709 1647 -5 131 +2 184604 2001
+4) 1735 1647 -5 131 +2 184592 1989
+5) 1836 1647 -5 131 +2 184590 1987
+Your choice (0 to stop):
+ at end group
+ at end example
+Entering 0 will stop the filtering procedure and output the current sequence selection. Possible choices are ordered according to the @command{comparison} option.
+In the above example, the current selection has 1,652 sequences and 129 sites with the given minimal coverage.
+Choice 1 proposes to remove 5 sequences, which would bring the total number of sequences to 1,647. This would gain 2 more sites with the required minimum coverage.
+Choice 2 also proposes to remove 5 sequences in order to add 2 more sites, but the total number of characters gained would be a bit lower. This means that even if both selection have the same number of sites, the ones in choice 1 have a higher coverage than the ones in choice 2. Picking option 1 leads to another proposal:
+ at example
+ at group
+Number of sequences in alignment.......: 1647
+Number of sites in alignment...........: 131
+Number of chars in alignment...........: 184714
+Choice Node #seq %seq #sites %sites #chars %chars
+1) 1930 1645 -2 132 +1 185794 1080
+2) 2246 1645 -2 132 +1 185792 1078
+3) 1950 1645 -2 132 +1 185788 1074
+4) 2093 1645 -2 132 +1 185786 1072
+5) 413 1645 -2 132 +1 185784 1070
+Your choice (0 to stop):
+ at end group
+ at end example
+and so on. The alogrithm ends either when the user enter '0' or when no more improving option exist.
+The number of proposal at each iteration can be specified using the @command{show=@{int>0@}} argument:
+ at command{method=Input(show=5)}.
+
+ at subsection Running mode: Diagnostic
+
+This mode will automatically pick the best choice at each iteration according to the @command{comparison} criterion until no more improving choice is proposed.
+The goal of this mode is mainly to plot a trade-off curve (see the example directory provided with the source code distribution).
+Only log files are produced, no sequence or tree output are written.
+
+ at subsection Running mode: Auto
+
+This mode works in a similar way as the Diagnostic mode, by picking the best choice at each iteration, but will stop when a given condition is reached and produce output alignments and trees.
+Currently two stopping conditions are implemented, which can be combined:
+
+ at table @command
+
+ at item min_nb_sequences=@{int>0@}
+will stop when no more improvement can be found or when all improving steps would bring the number of sequences below the given number.
+
+ at item min_relative_nb_sequences=@{int[0,1]@}
+will stop when no more improvement can be found or when all improving steps would bring the proportion of remaining sequences below the given threshold.
+This option only has an effect if min_nb_sequences is not set or set to 0.
+
+ at item min_nb_sites=@{int>0@}
+will stop when the number of sites matching the requested coverage is at least the given number.
+
+ at item min_relative_nb_sites=@{int[0,1]@}
+will stop when the number of sites matching the requested coverage is at least the given proportion of total alignment sites.
+This option only has an effect if min_nb_sites is not set or set to 0.
+
+ at end table
+
+For instance, @command{Auto(min_nb_sequences=100, min_nb_sites=300)} will stop the filtering when no improvement can be found, at least 300 sites have the minimum requested coverage or when there is no more than 200 sequences left.
+ at command{Auto(min_nb_sequences=100)} will perform all possible improvements which do not bring the final number of sequences below 100. @command{Auto(min_nb_sites=300)} will perform all possible improvements until 300 sites have the requested coverage. This might result in having only one sequence left in the output file.
+
+ at section Output files
+
+ at sc{bppalnoptim} generates several ouput files:
+
+ at table @command
+
+ at item output.log = @{path@}
+Logfile containing the characteristics of each iteration. This file can be used to plot the trade-off curve (see Diagnostic mode).
+
+ at end table
+
+The sampled alignment is written using the standard options in the BppO syntax (@ref{WritingSequences, , , bppsuite, @uref{http://biopp.univ-montp2.fr/manual/html/bppsuite/2.2.0/WritingSequences.html#WritingSequences}}).
+Optionally, the sampled tree can also be written using options from the BppO syntax (@ref{WritingTrees, , , bppsuite, @uref{http://biopp.univ-montp2.fr/manual/html/bppsuite/2.2.0/WritingTrees.html#WritingTrees}}).
+
+ at c ------------------------------------------------------------------------------------------------------------------
+
+ at c end of document
+
+ at c @node Index, , Reference, Top
+ at c @unnumbered Index
+ at c
+ at c @printindex cp
+
+ at bye
diff --git a/examples/PF01049/AlnOptimAuto.bpp b/examples/PF01049/AlnOptimAuto.bpp
new file mode 100644
index 0000000..9fce793
--- /dev/null
+++ b/examples/PF01049/AlnOptimAuto.bpp
@@ -0,0 +1,23 @@
+# Global variables:
+DATA = PF01049
+LINKAGE = complete
+
+# Input files and formats:
+alphabet = Protein
+input.sequence.file = $(DATA)_full.txt
+input.sequence.format = Fasta
+input.tree.method = AutoCluster(linkage=$(LINKAGE))
+
+# Selection parameters:
+filter_unresolved = yes #Tell if unresolved characters should also be filtered (just like gaps)
+threshold = 0.7 #Minimum proportion of characters per site
+method = Diagnostic #Input(show=10) #Input or Diagnostic
+comparison = MaxSites #MaxSites or MaxChars
+
+# Output files and formats:
+output.log = bppalnoptim_auto_$(LINKAGE).log
+output.sequence.file = $(DATA)_optimized_auto_$(LINKAGE).fasta
+output.sequence.format = Fasta
+output.tree.file = $(DATA)_optimized_auto_$(LINKAGE).dnd
+output.tree.format = Newick
+
diff --git a/examples/PF01049/AlnOptimFasttree.bpp b/examples/PF01049/AlnOptimFasttree.bpp
new file mode 100644
index 0000000..1d9c716
--- /dev/null
+++ b/examples/PF01049/AlnOptimFasttree.bpp
@@ -0,0 +1,24 @@
+# Global variables:
+DATA = PF01049
+
+# Input files and formats:
+alphabet = Protein
+input.sequence.file = $(DATA)_full.txt
+input.sequence.format = Fasta
+input.tree.method = File
+input.tree.file = $(DATA)_fasttree.dnd
+input.tree.format = Newick
+
+# Selection parameters:
+filter_unresolved = yes #Tell if unresolved characters should also be filtered (just like gaps)
+threshold = 0.7 #Minimum proportion of characters per site
+method = Diagnostic #Input(show=10) #Input or Diagnostic
+comparison = MaxSites #MaxSites or MaxChars
+
+# Output files and formats:
+output.log = bppalnoptim_fastml.log
+output.sequence.file = $(DATA)_optimized_fastml.fasta
+output.sequence.format = Fasta
+output.tree.file = $(DATA)_optimized_fastml.dnd
+output.tree.format = Newick
+
diff --git a/examples/PF01049/AlnOptimFasttreeStop.bpp b/examples/PF01049/AlnOptimFasttreeStop.bpp
new file mode 100644
index 0000000..d544d67
--- /dev/null
+++ b/examples/PF01049/AlnOptimFasttreeStop.bpp
@@ -0,0 +1,24 @@
+# Global variables:
+DATA = PF01049
+
+# Input files and formats:
+alphabet = Protein
+input.sequence.file = $(DATA)_full.txt
+input.sequence.format = Fasta
+input.tree.method = File
+input.tree.file = $(DATA)_fasttree.dnd
+input.tree.format = Newick
+
+# Selection parameters:
+filter_unresolved = yes #Tell if unresolved characters should also be filtered (just like gaps)
+threshold = 0.7 #Minimum proportion of characters per site
+method = Auto(min_nb_sequences=0, min_relative_nb_sequences=0.5) #Input or Diagnostic or Auto
+comparison = MaxSites #MaxSites or MaxChars
+
+# Output files and formats:
+output.log = bppalnoptim_fastml_stop.log
+output.sequence.file = $(DATA)_optimized_fastml.fasta
+output.sequence.format = Fasta
+output.tree.file = $(DATA)_optimized_fastml.dnd
+output.tree.format = Newick
+
diff --git a/examples/PF01049/PF01049_fasttree.dnd b/examples/PF01049/PF01049_fasttree.dnd
new file mode 100644
index 0000000..19ecf2d
--- /dev/null
+++ b/examples/PF01049/PF01049_fasttree.dnd
@@ -0,0 +1 @@
+(H0VDX1_CAVPO/636-783:0.00779,(CADH6_HUMAN/637-784:0.0,H2R1Q6_PANTR/629-776:0.0):0.00779,(((((Q5RCN5_PONAB/637-784:0.0,G1SD52_RABIT/637-784:0.0,H2PF91_PONAB/637-784:0.0):0.00054,(((CADH6_CHICK/637-784:0.0,G3UUF5_MELGA/637-784:0.0,G1K340_CHICK/562-709:0.0,G1N0W0_MELGA/635-782:0.0):0.01536,H0YUP1_TAEGU/637-784:0.00055)0.953:0.03917,(((G3WNM9_SARHA/637-784:0.0,F6Y191_MONDO/639-786:0.0):0.00055,H9GDM6_ANOCA/562-709:0.02403)0.754:0.01270,(((F7BE94_XENTR/641-788:0.00751,(Q9DFS0_XENLA/639-786:0 [...]
diff --git a/examples/PF01049/PF01049_full.txt b/examples/PF01049/PF01049_full.txt
new file mode 100644
index 0000000..cb94fae
--- /dev/null
+++ b/examples/PF01049/PF01049_full.txt
@@ -0,0 +1,19824 @@
+>H2TZ19_TAKRU/638-789
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------kRQR---KQEPL-----IISKE------DVR-D
+NVVSYNDEGGGEE------D-------------------------TQ-AFDIG--ALRHP
+QSTail-----------------------------------------eestKQRRDIIP-
+-T-G--L---L-M-PPVG--VPSR------------------------------------
+-----DNGDV-CE--FINQR-V-L-D-N-DCNPT---APPYDSLA------TYA---YEG
+AG-------------------------------------------------------SVA
+ES-LSSLG--S----------MS----SE--------A-DQ---------D---------
+----Y--QY-L-SDW-G-PRFRKLADLYGA-e----------------------------
+--------------------------------------------------------
+>Q5RCN5_PONAB/637-784
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------r-RQR--KKEPL-----IISKE------DIR-D
+NIVSYNDEGGGEE------D-------------------------TQ-AFDIG--TLRNP
+EAIe---------------------------------------------dnKLRRDIVP-
+-E-T--L---F-L-PRRT---PTA------------------------------------
+----RDNTDV-RD--FINQR-L-K-E-N-DTDPT---APPYDSLA------TYA---YEG
+TG-------------------------------------------------------SVA
+DS-LSSLE--S----------VT----TD--------G-DQ---------D---------
+----Y--DY-L-SDW-G-PRFKKLADMYGG-v----------------------------
+--------------------------------------------------------
+>B4KEF2_DROMO/4929-5081
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RKRKTTKKKK------RSGTEK-----DVR-E
+TVISYEDEGGGED------D-------------------------MT-AFDIT--PLQIP
+ISA-------------------------------------------------QSGTMPP-
+-D-I--A---A-C-KMPI--IYPVmtl---------------------------------
+-lppGQELNV-AY--LMEER-K-Q-R-I-DKDPN---APPFDDLR------NFT---FEG
+SG-------------------------------------------------------SIA
+ES-LSSLA--S----------GT----DD--------E-NQ---------D---------
+----F--NY-L-QNW-G-PRFNALAAMYVH-d----------------------------
+--------------------------------------------------------
+>E9Q451_MOUSE/645-745
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------r-RH---KNEPL-----IIKDDE-----DVR-E
+NIIRYDDEGGGEE------D-------------------------TE-AFDIA--TLQNP
+DGIn---------------------------------------------gfLPRKDIKP-
+-D-L--Q---F-M-PRLP--KRLP------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------krntrecclkkgtmdhsdfkekkisqdfk
+r-------------------------------------------------------
+>G5BP53_HETGA/443-591
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRQKKKD---S-----LMTSKE-----DVR-D
+NVIHYDDEGGGEE------D-------------------------TQ-AFDIG--ALRNP
+KAVe---------------------------------------------enKIRRDIKP-
+-D-S--L---C-L-PRQR--PGPV------------------------------------
+----EDNTDI-RD--FINQR-L-Q-E-N-DVDPT---APPYDSLA------TYA---YEG
+NG-------------------------------------------------------SAA
+ES-LSSID--S----------LT----TD--------T-DQ---------D---------
+----Y--DY-L-AEW-G-PRFKVLADMFGE-e----------------------------
+--------------------------------------------------------
+>Q5RD36_PONAB/638-785
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRQKKKD---T-----LMTSKE-----DIR-D
+NVIHYDDEGGGEE------D-------------------------TQ-AFDIG--ALRNP
+KVIe---------------------------------------------enKIRRDIKP-
+-D-S--L---C-L-PRQR--P-PV------------------------------------
+----EDNTDI-RD--FIHQR-L-Q-E-N-DVDPT---APPYDSLA------TYA---YEG
+SG-------------------------------------------------------SVA
+ES-LSSID--S----------LT----TE--------A-DQ---------D---------
+----Y--DY-L-TDW-G-PRFKVLADMFGE-e----------------------------
+--------------------------------------------------------
+>H2ZE81_CIOSA/642-792
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRRQQAGLEKE-----ILLDDD-----DVR-E
+NLQAYHDEGGGEE------D-------------------------ND-GYDIS--ALQAP
+PPNs---------------------------------------------vkPKVIDVRP-
+-L-G--G---A-Q-PESR--RPI-------------------------------------
+----QPDTDI-GN--YIGDA-K-Q-Q-A-DNDPT---APPFDSLL------VFD---YEG
+QG-------------------------------------------------------SDA
+GS-LSSIN--S----------GT----TD--------A-SQ---------D---------
+----Y--DY-L-NNW-G-PRFKKLADMYGG-g----------------------------
+--------------------------------------------------------
+>H2V7K2_TAKRU/562-720
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRQKRDSL--------SPLEED-----DVR-E
+NIITYDDEGGGEA------D-------------------------TA-AFDIA--ALQSA
+PHSsrsr---------------------------------------gyrtlDSRNVFIP-
+-G-M--E---A------------Argap-------------------------------g
+ssgpSLALRV-GE--FLRLR-L-A-Q-V-TFDPS---QPPYDSVQ------VYG---LEG
+TG-------------------------------------------------------SRA
+GS-LSSLE-sE----------GE---kDT--------E-KE---------E---------
+----W--GTgL-EEW-G-PQFQKLAQLFKD-r----------------------------
+--------------------------------------------------------
+>F6XSE3_MONDO/697-787
+------------------------------------------------------------
+------------------------------------------------------------
+------tlrrnsmrecregglnmnfmes--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------Y--FCQKA-F-A-Y-A-DEDES---RPSNDCLL------IYD---IEG
+VG-------------------------------------------------------SSA
+GS-IG-----C----------CS---fIG--------E-DL---------D---------
+----D--SF-L-DNL-G-PKFKKLADI----slgk-------------------------
+--------------------------------------------------------
+>H0VE04_CAVPO/592-741
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------vr---KKRKVKEP-----LLLPED-----DTR-D
+NVFYYGEEGGGEE------D-------------------------QD--YDIT--QLHRG
+LEArp--------------------------------------------evVLRNDVAP-
+-T-F--M---P-T-PMYR---PRP------------------------------------
+----ANPDEI-GN--FIIEN-L-K-A-A-NTDPT---APPYDSLL------VFD---YEG
+SG-------------------------------------------------------SEA
+AS-LSSLT--S----------SD----QD--------R-DQ---------D---------
+----Y--DY-L-NEW-G-SRFKKLADMYGG-g----------------------------
+--------------------------------------------------------
+>C3Y3A1_BRAFL/2734-2841
+------------------------------------------------------------
+----------------------------------------------------------fs
+sstdmlavrnknpaivcsvaptlppppp--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-S-N--S---A-S----------Dsdsiq-----------------------------kp
+awefECPNVV-EG--YVESK-V-N-D-A-DAVMN---NIANDEMQ------VYR---NEG
+GS------------------------------------------------------mTDM
+VS-LSSLP--S----------ES----CD--------E-D--------------------
+-------------------------------nmpvs------------------------
+--------------------------------------------------------
+>F6SF63_XENTR/565-713
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------r-RH---KNEPL-----IIKDDE-----DVR-E
+NIIRYDDEGGGEE------D-------------------------TE-AFDIA--TLQNP
+DGIn---------------------------------------------gyLPRKDIKP-
+-D-F--Q---F-M-PRQG--HTST------------------------------------
+----PNGVDV-DE--FINVR-L-H-E-A-DNDPT---APPYDSIQ------IYG---YEG
+RG-------------------------------------------------------SVA
+GS-LSSLE--S----------SA----SD--------S-DQ---------N---------
+----F--DY-L-TDW-G-PRFKRLGELYS--vg---------------------------
+--------------------------------------------------------
+>G1KN84_ANOCA/564-712
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRRKKE---PL-----VFDEER-----DIR-E
+NIVRYDDEGGGEE------D-------------------------TE-AFDMA--ALRNL
+NIIr---------------------------------------------dtKTRRDVTP-
+-E-I--Q---F-L-SRPS--FKSI------------------------------------
+----PDNVIF-RE--FIWER-L-K-E-A-DVDPC---APPYDSLQ------TYA---FEG
+NG-------------------------------------------------------SVA
+ES-LSSLD--S----------IS----SN--------S-DQ---------N---------
+----Y--DY-L-SDW-G-PRFKRLADMYGT-g----------------------------
+--------------------------------------------------------
+>G3NM78_GASAC/623-779
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------rddapeaegap-----------------DEEER-----DIR-E
+NIVRYDDEGGGEE------D-------------------------TE-AFDMV--TLRNL
+NAIr---------------------------------------------dpGARRDVTP-
+-D-T--P---T-F-FRYT--STARpay---------------------------------
+-kslPDNVVF-RE--FIWER-L-K-D-A-DVDSS---APPYDSLQ------TYA---FEG
+SG-------------------------------------------------------SVA
+ES-LSSLE--S----------LS----TD--------S-EQ---------N---------
+----Y--DY-L-SNW-G-PRFKKLADLYGN-g----------------------------
+--------------------------------------------------------
+>CADH9_HUMAN/637-784
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------kr-QR---KKEPL-----IIS-KD-----DVR-D
+NIVTYNDEGGGEE------D-------------------------TQ-AFDIG--TLRNP
+EARe---------------------------------------------dsKLRRDVMP-
+-E-T--I---F-Q-IRRT--VPLW------------------------------------
+-----ENIDV-QD--FIHRR-L-K-E-N-DADPS---APPYDSLA------TYA---YEG
+ND-------------------------------------------------------SIA
+DS-LSSLE--S----------LT----AD--------C-NQ---------D---------
+----Y--DY-L-SDW-G-PRFKKLADMYGG-d----------------------------
+--------------------------------------------------------
+>CAD20_XENLA/635-784
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------mr-RHR---KQPY-----TIDEED-----NVH-E
+NIVRYDDEGGGEE------D-------------------------TE-AFDIA--ALWNP
+REAh---------------------------------------------mgKTRQDMKP-
+-E-I--E---S-L-SRYV--TQTC------------------------------------
+----RMDNNV-HS--YMLAK-L-Y-E-A-DTDVC---APPFDSLQ------TYM---FEG
+EG-------------------------------------------------------SVA
+HS-LSSLQ--S----------LS----TD--------S-EQ---------S---------
+----Y--DY-L-SDW-G-PRFKKLAEMYGT-k----------------------------
+--------------------------------------------------------
+>F7HFS5_CALJA/158-309
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRQKQE---AL-----MVLEEE-----DVR-E
+NIITYDDEGGGEE------D-------------------------TE-AFDIT--ALQNP
+DGAapp-----------------------------------------apgpPARRDVLP-
+-R-S--R---V-P-RQ-----PRP------------------------------------
+----PGPADV-AQ--LLALR-L-R-E-A-DEDPS---VPPYDSVQ------VYG---YEG
+RG-------------------------------------------------------SSC
+GS-LSSLG--S----------GS----EA--------G-GIp-------gP---------
+----A--EP-L-DDW-G-PLFRTLAELYGA-k----------------------------
+--------------------------------------------------------
+>F1NHU4_CHICK/714-786
+------------------------------------------------------------
+------------------------------------------------------------
+----------------fldnyfsekafv--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------Y-A-DEDEG---RPANDCLL------IYD---HEG
+IG-------------------------------------------------------TPV
+GS-VG-----C----------CS---fIG--------E-DT---------D---------
+----E--TY-L-ETL-G-PKFKTLAEICL--gk---------------------------
+--------------------------------------------------------
+>H9GPT4_ANOCA/783-862
+------------------------------------------------------------
+------------------------------------------------------------
+-----------smvnedflrsyftvkae--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------A-F-A-DEDET---QLAKDCLL------VYS--qDEE
+KD-------------------------------------------------------SIR
+GS-VG-----C----------CS---fIE--------D-DF---------D---------
+----D--HF-L-DDL-G-DKFKTLAEICMG-k----------------------------
+--------------------------------------------------------
+>E9J709_SOLIN/1157-1269
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------hrrk--------TDD-----LYKDMD-----DIR-E
+NIINYEDEGGGEG------D-------------------------VQ-GYDLN--VLRAI
+YDA-----------------------------------------------pPIDSKIAP-
+-V-G--L---Q-----------GRg-----------------------------------
+---tDEVPDI-CG--FLDGK-K-E-S-C-DKDPD---TNPFDDVR------HYA---YEG
+EG-------------------------------------------------------NSE
+GD-LSSLA--S----------C--------------------------------------
+------------------------------------------------------------
+--------------------------------------------------------
+>H2NW47_PONAB/695-797
+------------------------------------------------------------
+-----------------------------------------------------ttettkt
+tratgasrdmagaqaaavalneeflrny--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------FTDKA-A-S-Y-T-EEDEN---HTAKDCLL------VYS---QEE
+TE-------------------------------------------------------SLN
+AS-IG-----C----------CS---fIE--------G-EL---------D---------
+----D--RF-L-DDL-G-LKFKTLAEVCL--gq---------------------------
+--------------------------------------------------------
+>H2V7K9_TAKRU/795-851
+------------------------------------------------------------
+------------------------------------------------------------
+--------wvpgmeaargapgssgpsla--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------LRV-GE--FLRLR-L-A-Q-V-TFDPS---QPPYDSVQ------VYG---LEG
+TG-------------------------------------------------------S--
+------------------------------------------------------------
+-------------------------------r----------------------------
+--------------------------------------------------------
+>H2RZR9_TAKRU/737-883
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------r-RRRGVKKEPL-------LQDT-----DVR-D
+NIFYYDEEGGGED------D-------------------------QD--YDLG--VLHRG
+LDNr---------------------------------------------peVFRNDVVP-
+-N-F--M---P-A-PQYQ---PRP------------------------------------
+----ANPEEI-GN--FIDHN-L-K-A-A-DNDPT---APPYDSLL------VFD---YEG
+GG-------------------------------------------------------SES
+GS-LSSLN--S----------SN-----S--------G-DQ---------D---------
+----Y--EC-L-SEW-G-PRFKKLADMYGG-g----------------------------
+--------------------------------------------------------
+>G1KRI0_ANOCA/3033-3143
+------------------------------------------------------------
+-------------------------------------------------------dsgip
+rdsdqlscqsgetdvvvvsqsveadhpf--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----KNESGG-EK--MLSQT-L-E-E-M-GIKEK---DITRDY--------VFV---PSG
+LN-------------------------------------------------------SHY
+GS-LATLA-aS----------DE---dLR--------G-SC---------S---------
+----W--DY-L-LNW-E-PRFKPLASVFS--di---------------------------
+--------------------------------------------------------
+>Q4S5K3_TETNG/600-756
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------kRREKERQNKQL-----LIDPED-----DVR-D
+NILKYDEEGGGEE------D-------------------------QD--YDLS--QLQQP
+DSLehii---------------------------------------skppgVRRVDERP-
+-I-I--P---E-S-QYPI--RPVV------------------------------------
+----PHPGDI-GD--FIHEG-L-R-A-A-DNDPT---APPYDSLL------VFD---YEG
+SG-------------------------------------------------------STA
+GS-VSSLN--S----------SS----T---------G-DQ---------D---------
+----Y--DY-L-NDW-G-PRFKKLADMYGG-g----------------------------
+--------------------------------------------------------
+>G1RUL4_NOMLE/637-784
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------r-RQR--KKEPL-----IISKE------DIR-D
+NIVSYNDEGGGEE------D-------------------------TQ-AFDIG--TLRNP
+EAIe---------------------------------------------dnKLRRDIVP-
+-E-A--L---F-L-PRRT---PTA------------------------------------
+----RDNTDV-RD--FINQR-L-K-E-N-DTDPT---APPYDSLA------TYA---YEG
+TG-------------------------------------------------------SVA
+DS-LSSLE--S----------VT----TD--------G-DQ---------D---------
+----Y--DY-L-SDW-G-PRFKKLADMYGG-v----------------------------
+--------------------------------------------------------
+>G7NKJ3_MACMU/717-894
+------------------------------------------------------------
+------krtvkkcfpediaqqnlivsntegpgeevteanirlpmqtsnicdtsmsvgtvg
+gqgiktqqsfemvkggytldsskggghq--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-----------------------Tlesvkgvg-----------------------qgdtg
+ryayTDWQSFtQP--RLGEK-V-Y-L-C-GQDEE--hKHCEDYVR------SYN---YEG
+KG-------------------------------------------------------SLA
+GS-VG-----C----------CS---dRQ--------E-EE---------G---------
+----L--EF-L-DQL-E-PKFRTLAKTCVK-k----------------------------
+--------------------------------------------------------
+>F6QW97_XENTR/738-813
+------------------------------------------------------------
+------------------------------------------------------------
+-------------degfireyfsdkafg--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------Y-S-DEDQA---QPAKDCIL------TYT---QED
+AG-------------------------------------------------------SLS
+GS-VG-----C----------CS---fIE--------S-EF---------D---------
+----Y--DC-L-DDL-G-MKFKALADICQ--gm---------------------------
+--------------------------------------------------------
+>H0ZK89_TAEGU/743-816
+------------------------------------------------------------
+------------------------------------------------------------
+---------------afldnyfsekafv--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------Y-A-DEDEG---RPANDCLL------IYD---HEG
+VG-------------------------------------------------------TPV
+GS-VG-----C----------CS---fIG--------E-DT---------D---------
+----E--TY-L-DTL-G-PKFKTLAEICL--gk---------------------------
+--------------------------------------------------------
+>CAD11_CHICK/636-785
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------lkr-----QKKEPL-----IVFEEE-----DVR-E
+NIITYDDEGGGEE------D-------------------------TE-AFDIA--TLQNP
+DGIn---------------------------------------------gfIPRKDIKP-
+-E-Y--Q---Y-M-PRPG--LRPA------------------------------------
+----PNSVDV-DD--FINTR-I-Q-E-A-DNDPT---APPYDSIQ------IYG---YEG
+RG-------------------------------------------------------SVA
+GS-LSSLE--S----------AT----TD--------S-DL---------D---------
+----Y--DY-L-QNW-G-PRFKKLADLYGS-k----------------------------
+--------------------------------------------------------
+>G1N8V3_MELGA/558-707
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------ir----QQRKKTL-----FPEKVE-----EFR-E
+NIVKYDDEGGGEE------D-------------------------TE-AFDIS--ALRTR
+TVLr---------------------------------------------thKPRKKITT-
+-E-I--H---S-L-YRQS--LQVG------------------------------------
+----PDSAIF-RQ--FISEK-L-E-E-A-NTDPS---APPYDSLQ------TYA---FEG
+TG-------------------------------------------------------SLA
+GS-LSSLG--S----------NM----SD--------A-DQ---------N---------
+----Y--DY-L-VGW-G-PHFKQLAGMYAS-q----------------------------
+--------------------------------------------------------
+>H2LH69_ORYLA/3052-3127
+------------------------------------------------------------
+------------------------------------------------------------
+-lpvyrdegggylgvgrglnislpkdya--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------------------FP---EDG
+KP-------------------------------------------------------SVD
+GS-LTAIV-aS----------DE---eLR--------G-SY---------N---------
+----W--DY-L-LNW-C-PQFQPLANVFTE-i----------------------------
+--------------------------------------------------------
+>E1FNG7_LOALO/1017-1143
+------------------------------------------------------------
+------------------------------------------------------------
+------------------rrhtppfepv------------------RPEE-----LNR-D
+NLRPYDLEGGGEA------D-------------------------ND-QYNIT--NLRKP
+VMP--------------------------------------------------IEENGV-
+-N-G--Y---A-Q-PVYP------------------------------------------
+----MQRAPI-DD--KLNSR-I-K-N-L-EADPD---ATAPITLE------SLE---STD
+DA-------------------------------------------------------APS
+GS-LD-----------------------------------Q-------------------
+--------E-I-EKW-G-PRFNNLADIYGKR-----------------------------
+--------------------------------------------------------
+>Q5XG31_XENLA/29-186
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------kRRDKERQAKQL-----LIDPED-----DVR-D
+NILKYDEEGGGEE------D-------------------------QD--YDLS--QLQQP
+DTMepdt---------------------------------------ikpvgIRRMDERP-
+-I-H--A---E-S-QYPI--RSAA------------------------------------
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+------------------------------------------------------------
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+>DSG1C_MOUSE/605-734
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+----E--SF-L-DTL-G-PKFKKLADI----slgk-------------------------
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+------------------------------------------------------------
+------------------------------------------------------------
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+NILKYDEEGGGEE------D-------------------------QD--YDLS--QLQQP
+ETM---------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------dhvlnktpgvr------------------
+--------------------------------------------------------
+>F8W7U2_HUMAN/790-914
+------------------------------------------------------------
+------------------------------------------------------------
+---------------knggqetiemvkg----------------GHQTSE-----SCRgA
+GHHHTLDSCRGGHt---evD-------------------------NC-RYTYS--EWHSF
+TQP---------------------------------------------------------
+------------------------------------------------------------
+---------------RLGEK-V-Y-L-C-NQDEN--hKHAQDYVL------TYN---YEG
+RG-------------------------------------------------------SVA
+GS-VG-----C----------CS---eRQ--------E-ED---------G---------
+----L--EF-L-DNL-E-PKFRTLAEACMK-r----------------------------
+--------------------------------------------------------
+>F6XSF2_MONDO/697-787
+------------------------------------------------------------
+------------------------------------------------------------
+------tlrrnsmrecregglnmnfmes--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------Y--FCQKA-F-A-Y-A-DEDES---RPSNDCLL------IYD---IEG
+VG-------------------------------------------------------SSA
+GS-IG-----C----------CS---fIG--------E-DL---------D---------
+----D--SF-L-DNL-G-PKFKKLADI----slgk-------------------------
+--------------------------------------------------------
+>O15941_BOMMO/1-103
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------GGEG------D--------------------------A-GYDLH--VLRQM
+YDG------------------------------------------------------PP-
+-P-D--T---G-A-YQQR--RLLL------------------------------------
+----ETTPDI-SG--FLDDK-K-S-V-L-DRDPD---IIPYDDVR------HYA---YEG
+DG-------------------------------------------------------NTS
+GS-LSSLA--S----------CT----DD--------E-DL---------K---------
+----F--NY-L-STF-G-PRFR--------------------------------------
+--------------------------------------------------------
+>G5AL48_HETGA/645-793
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------r-RH---KNEPL-----IIKDDE-----DVR-E
+NIIRYDDEGGGEE------D-------------------------TE-AFDIA--TLQNP
+DGIn---------------------------------------------gfLPRKDIKP-
+-D-L--Q---F-M-PRQG--LAPV------------------------------------
+----PNGVDV-DE--FINVR-L-H-E-A-DNDPT---APPYDSIQ------IYG---YEG
+RG-------------------------------------------------------SVA
+GS-LSSLE--S----------TT----SD--------S-DQ---------N---------
+----F--DY-L-SDW-G-PRFKRLGELYS--vg---------------------------
+--------------------------------------------------------
+>G3QD69_GORGO/703-859
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------kRREKERHTKQL-----LIDPED-----DVR-D
+NILKYDEEGGGEE------D-------------------------QD--YDLS--QLQQP
+EAMghvp---------------------------------------skapgVRRVDERP-
+-V-G--A---E-P-QYPI--RPMV------------------------------------
+----PHPGDI-GD--FINEG-L-R-A-A-DNDPT---APPYDSLL------VFD---YEG
+SG-------------------------------------------------------STA
+GS-VSSLN--S----------SS----S---------G-DQ---------D---------
+----Y--DY-L-NDW-G-PRFKKLADMYGG-g----------------------------
+--------------------------------------------------------
+>H2T5R8_TAKRU/691-782
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------kRRDKERQAKQL-----LIDPED-----DVR-D
+NILKYDEEGGGEE------D-------------------------QD--YDLS--QLQQP
+DTLepda---------------------------------------ikpvgIRRLDERP-
+-L-H--P---E-P-QYPM--RSAA------------------------------------
+----PHPGDI-GD--FINE-----------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------------------------------------
+>F7EML7_CALJA/625-776
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRQKQE---AL-----MVLEEE-----DVR-E
+NIITYDDEGGGEE------D-------------------------TE-AFDIT--ALQNP
+DGAapp-----------------------------------------apgpPARRDVLP-
+-R-S--R---V-P-RQ-----PRP------------------------------------
+----PGPADV-AQ--LLALR-L-R-E-A-DEDPS---VPPYDSVQ------VYG---YEG
+RG-------------------------------------------------------SSC
+GS-LSSLG--S----------GS----EA--------G-GIp-------gP---------
+----A--EP-L-DDW-G-PLFRTLAELYGA-k----------------------------
+--------------------------------------------------------
+>F6WVN9_XENTR/587-733
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------klkk-------KHTT-----LSEKSE-----DFR-E
+NIVKYDDEGGGEE------D-------------------------TE-AFDIG--HLTNQ
+AIL---------------------------------------------------RKQKP-
+-R-N--R---R-F-RTDI--QSFYrms---------------------------------
+lklgPDIAVF-KE--FLLEK-L-E-E-A-NEDIE---SLPLDSLK------TYA---FEG
+TG-------------------------------------------------------SLA
+GS-LSSIE--S----------AF----SD--------I-DP---------N---------
+----I--QN-I-CDW-K-L------------qiqsfpeth--------------------
+--------------------------------------------------------
+>Q4SNR1_TETNG/799-854
+------------------------------------------------------------
+------------------------------------------------------------
+--------vpgmeaargapgtggpslal--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+--------RV-GE--FLRLR-L-A-Q-V-TFDPS---QPPYDSVQ------VYG---LEG
+TG-------------------------------------------------------S--
+------------------------------------------------------------
+-------------------------------r----------------------------
+--------------------------------------------------------
+>H2LVV1_ORYLA/623-759
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------rcr---KQQ---TR-----ILDHEQ-----DIQ-E
+NIVYCDDEGGGEE------D-------------------------TE-AFDIT--ALRHL
+NQT-------------------------------------------------KLTSRLP-
+-N-S------------------GT------------------------------------
+----ERHRMI-QE--FIRDR-L-Q-V-A-DQDLT---APPFDSLQ------TYN---FEG
+VG-------------------------------------------------------SAA
+VS-LSSLN-sQ----------DS----GE--------S-EG---------G---------
+----Y--SF-L-KEW-G-PRFRKLAELYSH-n----------------------------
+--------------------------------------------------------
+>F7ITB7_CALJA/583-730
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------kr-QR---KKEPL-----IIS-KD-----DVR-D
+NVVTYNDEGGGEE------D-------------------------TQ-AFDIG--TLRNP
+EARe---------------------------------------------dsKLRRDVMP-
+-E-T--I---F-Q-IRRT--VPLW------------------------------------
+-----ENIDV-QD--FIHRR-L-K-E-N-DADPS---APPYDSLA------TYA---YEG
+ND-------------------------------------------------------SIA
+DS-LSSLE--S----------LT----VD--------C-NQ---------D---------
+----Y--DY-L-SDW-G-PRFKKLADMYGG-d----------------------------
+--------------------------------------------------------
+>H9GPS3_ANOCA/794-894
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------ghqtlesvk--------------------------------
+--------GYGQNm----mD-------------------------TY-RYNYS--EWQNF
+THP---------------------------------------------------------
+------------------------------------------------------------
+---------------RLTEK-V-Y-L-C-GQDEE--hKHSDDYIL------SYN---YEG
+RG-------------------------------------------------------SPA
+GS-IG-----C----------CT---dHQ--------E-EE---------A---------
+----L--DF-L-DQL-E-PKFRTLAETCVK-r----------------------------
+--------------------------------------------------------
+>B3DJF6_DANRE/615-759
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRRYQKE--VL-----VTKASG-----EIH-E
+QLVRYDEEGGGEM------D-------------------------TN-GYDVS--ILSSA
+CHD-----------------------------------------------sSFRPSVGP-
+-A-L--Y---A-M-VKKP-----P------------------------------------
+----ACKGDM-AM--MIEVK-K-D-E-A-DRDRD---GIPYDTLH------IYG---YEG
+TE-------------------------------------------------------SLA
+GS-LSSLD--S----------SS----SG--------S-NL---------D---------
+----Y--DF-I-HEW-G-PRFRTLAQLYG--vd---------------------------
+--------------------------------------------------------
+>G3VXU4_SARHA/647-721
+------------------------------------------------------------
+------------------------------------------------------------
+--------------fsfiicfkkskafa--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------Y-A-DEDEG---RPSNDCLL------IYD---IEG
+VG-------------------------------------------------------SSA
+GS-IG-----C----------CS---fIG--------E-DE---------D---------
+----D--SF-L-DTL-G-PKFKKLADI----slgk-------------------------
+--------------------------------------------------------
+>G3W7N1_SARHA/631-779
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRRKKE---PL-----IFDEER-----DIR-E
+NIVRYDDEGGGEE------D-------------------------TE-AFDMA--ALRNL
+NVIr---------------------------------------------dtKTRRDVTP-
+-E-I--Q---F-L-SRPT--FKSI------------------------------------
+----PDNVIF-RE--FIWER-L-K-E-A-DIDPC---APPYDSLQ------TYA---FEG
+NG-------------------------------------------------------SVA
+ES-LSSLD--S----------IS----SN--------S-DQ---------N---------
+----Y--DY-L-SDW-G-PRFKRLADMYGT-s----------------------------
+--------------------------------------------------------
+>G1N1H4_MELGA/638-785
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRQKKKD---T-----LMTSKE-----DIR-D
+NVIHYDDEGGGEE------D-------------------------TQ-AFDIG--ALRNP
+KAIe---------------------------------------------dnKMRRDIKP-
+-D-T--L---R-F-PRQR--AP-V------------------------------------
+----EDNTDI-RD--FINQR-L-Q-E-N-DVDPT---APPYDSLA------TYA---YEG
+NG-------------------------------------------------------SVA
+ES-LSSIE--S----------LT----TE--------A-DQ---------D---------
+----Y--DY-L-SDW-G-PRFKILADMFGE-e----------------------------
+--------------------------------------------------------
+>H2TX10_TAKRU/728-884
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------kRREKERQAKPL-----LIDPED-----DVR-D
+NILKYDEEGGGEE------D-------------------------QD--YDLS--QLQQP
+ESLdhii---------------------------------------nkpagVRRVDERP-
+-A-I--A---E-S-QYPV--RSSL------------------------------------
+----PHPGDI-GD--FINDG-L-R-A-A-DNDPT---APPYDSLL------VFD---YEG
+TG-------------------------------------------------------STA
+GS-VSSLN--S----------IS----S---------G-DQ---------D---------
+----Y--DY-L-NDW-G-PRFKKLADLYGG-g----------------------------
+--------------------------------------------------------
+>Q8C5C8_MOUSE/93-216
+------------------------------------------------------------
+---------------------------------------ggqetiemvkggqqtldsrrg
+agyhhhtldpcrgghvevdnyrhtysew--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------YNFI-QP--RLGDK-V-Q-F-C-HTDDN--qKLAQDYVL------TYN---YEG
+KG-------------------------------------------------------SAA
+GS-VG-----C----------CS---dLQ--------E-ED---------G---------
+----L--EF-L-DHL-E-PKFRTLAEVCAK-r----------------------------
+--------------------------------------------------------
+>F1NUS5_CHICK/580-727
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRRKVEK--EP-----LLPPED-----DMR-D
+NVYNYDEEGGGEE------D-------------------------QD--YDLS--QLHRG
+LDAr---------------------------------------------peVIRNDVAP-
+-P-L--M---A-A-PQYR---PRP------------------------------------
+----ANPDEI-GN--FIDEN-L-K-A-A-DTDPT---APPYDSLL------VFD---YEG
+GG-------------------------------------------------------SEA
+TS-LSSLN--S----------SA----SD--------Q-DQ---------D---------
+----Y--DY-L-NEW-G-NRFKKLAELYGG-g----------------------------
+--------------------------------------------------------
+>G7NKJ7_MACMU/755-858
+------------------------------------------------------------
+-------------------------------------------------mttettkttra
+tgasrdmagaqaaavalneeflrnyfsd--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------KA-A-S-Y-T-EEDEN---HTAKDCLL------VYS---QEE
+TE-------------------------------------------------------SLN
+AS-IG-----C----------CS---fIE--------G-EL---------D---------
+----D--RF-L-DDL-G-LKFKTLAEVCL--gq---------------------------
+--------------------------------------------------------
+>G7P7A9_MACFA/637-784
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------r-RQR--KKEPL-----IISKE------DIR-D
+NIVSYNDEGGGEE------D-------------------------TQ-AFDIG--TLRNP
+EAIe---------------------------------------------dnKLRRDIVP-
+-E-A--L---F-L-PRRT---PTA------------------------------------
+----RDNTDV-RD--FINQR-L-K-E-N-DTDPT---APPYDSLA------TYA---YEG
+TG-------------------------------------------------------SVA
+DS-LSSLE--S----------VT----TD--------G-DQ---------D---------
+----Y--DY-L-SDW-G-PRFKKLADMYGG-v----------------------------
+--------------------------------------------------------
+>F7AAP1_MONDO/638-785
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRQKKKD---T-----LMTSKE-----DIR-D
+NVIHYDDEGGGEE------D-------------------------TQ-AFDIG--ALRNP
+KVIe---------------------------------------------dnKMRRDIKP-
+-D-T--L---C-L-PRQR--P-PV------------------------------------
+----EDNTDI-RD--FIHQR-L-Q-E-N-DGDPT---APPYDSLA------TYA---YEG
+NG-------------------------------------------------------SVA
+ES-LSSID--S----------GT----TE--------A-DQ---------D---------
+----Y--DY-L-TDW-G-PRFKILADMFGE-e----------------------------
+--------------------------------------------------------
+>H2V7K8_TAKRU/583-664
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRQKRDSL--------SPLEED-----DVR-E
+NIITYDDEGGGEA------D-------------------------TA-AFDIA--ALQSA
+PHS------------------------------------------------SRSRGYRT-
+-L-D--S---R-N-V---------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------ryalrtqdkcptyswaqnpav--------
+--------------------------------------------------------
+>Q5RB18_PONAB/716-873
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------kRRDKERQAKQL-----LIDPED-----DVR-D
+NILKYDEEGGGEE------D-------------------------QD--YDLS--QLQQP
+DTVepda---------------------------------------ikpvgIRRMDERP-
+-I-H--A---E---PQYP--VRSA------------------------------------
+---aPHPGDI-GD--FINEG-L-K-A-A-DNDPT---APPYDSLL------VFD---YEG
+SG-------------------------------------------------------STA
+GS-LSSLN--S----------SS----SG--------G-EQ---------D---------
+----Y--DY-L-NDW-G-PRFKKLADMYGG-g----------------------------
+--------------------------------------------------------
+>G3HFU2_CRIGR/565-713
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRRKKE---PL-----IFDEER-----DIR-E
+NIVRYDDEGGGEE------D-------------------------TE-AFDMA--ALRNL
+NVIr---------------------------------------------dnKTRRDVTP-
+-E-I--Q---F-L-SRPT--FKSI------------------------------------
+----PDNVIF-RE--FIWER-L-K-E-A-DVDPG---APPYDSLQ------TYA---FEG
+NG-------------------------------------------------------SVA
+ES-LSSLD--S----------IS----SN--------S-DQ---------N---------
+----Y--DY-L-SDW-G-PRFKRLADMYGN-g----------------------------
+--------------------------------------------------------
+>A3KQ94_DANRE/547-690
+------------------------------------------------------------
+------------------------------------------------------------
+--------------------------kr--RCGRKFQQ-------FTKNE-----EDR-D
+NIICYNEEGGGEQ------D-------------------------QD--FDIM--LLCGG
+PEV-------------------------------------------------FYRDIAP-
+-T-V--L---P-T-VVYR--QLP-------------------------------------
+----EEDEDM-EN--FIYEN-L-C-T-A-DDEHY---VAPFDSVL------VFA---HEG
+EG-------------------------------------------------------SKA
+GS-LSSIQ--S----------SI----SD--------G-GL---------E---------
+----F--QD-L-HSW-G-PPFRRLADLYAE-r----------------------------
+--------------------------------------------------------
+>Q9W6G5_DANRE/331-487
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------kRREKERQTKPL-----LIDPED-----DVR-D
+NILKYDEEGGGEE------D-------------------------QD--YDLS--QLQQP
+ESLdhim---------------------------------------skpagVRRVDERP-
+-V-I--L---E-S-QYPV--RPTV------------------------------------
+----PHPGDI-GE--FITDG-L-R-A-A-DNDPT---APPYDSLL------VFD---YEG
+SG-------------------------------------------------------STA
+GS-VSSLD--S----------SS----S---------G-EQ---------D---------
+----Y--DY-L-NDW-G-PRFKKLADLYGG-g----------------------------
+--------------------------------------------------------
+>G3RM70_GORGO/570-741
+------------------------------------------------------------
+------------------------------------------------------------
+---------------------------r-RHHKS---HL-----SSDEDE-----DMR-D
+NVIKYNDEGGGEQ------D-------------------------TE-AYDMS--ALRSL
+YDFgelkggdgggsa-----------------------gggagggsgggagSPPQAHLP-
+-S-E--R---HsL-PQGP--PSPE------------------------------------
+----PDFSVF-RD--FISRK-V-A-L-A-DGDLS---VPPYDAFQ------TYA---FEG
+AD-------------------------------------------------------SPA
+AS-LSSLH--S----------GS----SG--------S-EQ---------D---------
+----F--AY-L-SSW-G-PRFRPLAALYAG-h----------------------------
+--------------------------------------------------------
+>G1R3U9_NOMLE/737-842
+------------------------------------------------------------
+--------------------------------------------------aimttetmkt
+tratgasrdmagaqaaavalneeflrny--------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+---------------FTDKA-A-S-Y-T-EEDEN---HTAKDCLL------VYS---QEE
+TE-------------------------------------------------------SLN
+AS-IG-----C----------CS---fIE--------G-EL---------D---------
+----D--RF-L-DDL-G-LKFKTLAEVCL--gq---------------------------
+--------------------------------------------------------
+>H3CR87_TETNG/578-660
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------RRQKRDSL--------SPLEED-----DVR-E
+NIITYDDEGGGEA------D-------------------------TA-AFDIA--ALQSA
+PHSsr-------------------------------------------srgY-----RT-
+-L-D--S---R-N-VRYA------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------------hrsqdkapnyswaqnpave----------
+--------------------------------------------------------
+>G7PW76_MACFA/618-767
+------------------------------------------------------------
+------------------------------------------------------------
+-------------------------lkq--R---RKQIL-----FPEKSE-----DFR-E
+NIFRYDDEGGGEE------D-------------------------TE-AFDVA--ALRSS
+TIMr---------------------------------------------erKTRKTTSA-
+-E-I--R---S-L-YRQS--LQVG------------------------------------
+----PDSAIF-RK--FILEK-L-E-E-A-DTDPC---APPFDSLQ------TYA---FEG
+TG-------------------------------------------------------SLA
+GS-LSSLE--S----------AV----SD--------Q-DE---------S---------
+----Y--DY-L-NEL-G-PRFKRLACMFGS-a----------------------------
+--------------------------------------------------------
diff --git a/examples/PF01049/README b/examples/PF01049/README
new file mode 100644
index 0000000..e5cc926
--- /dev/null
+++ b/examples/PF01049/README
@@ -0,0 +1,12 @@
+# Created on 24/10/14 by jdutheil
+
+bppalnoptim param=AlnOptimFasttree.bpp
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=complete
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=single
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=average
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=median
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=centroid
+bppalnoptim param=AlnOptimAuto.bpp LINKAGE=ward
+
+#Get a selection of sequences:
+bppalnoptim param=AlnOptimFasttreeStop.bpp
diff --git a/examples/PF01049/diagnostic.R b/examples/PF01049/diagnostic.R
new file mode 100644
index 0000000..481c178
--- /dev/null
+++ b/examples/PF01049/diagnostic.R
@@ -0,0 +1,60 @@
+# Created on 09/10/14 by jdutheil
+library(RColorBrewer)
+cols<-brewer.pal(6, name="Accent")
+
+read.profile<-function(file) {
+ dat <- read.table(file, header=TRUE)
+ dat$relSeq <- cumsum(-dat$DiffSequences) / dat[1, "NbSequences"]
+ dat$relSit <- cumsum(dat$DiffSites) / dat[nrow(dat), "NbSites"]
+ return(dat)
+}
+
+dat<-read.profile("bppalnoptim_fastml.log")
+dat.a1<-read.profile("bppalnoptim_auto_complete.log")
+dat.a2<-read.profile("bppalnoptim_auto_single.log")
+dat.a3<-read.profile("bppalnoptim_auto_average.log")
+dat.a4<-read.profile("bppalnoptim_auto_median.log")
+dat.a5<-read.profile("bppalnoptim_auto_centroid.log")
+dat.a6<-read.profile("bppalnoptim_auto_ward.log")
+re<-range(dat$NbSequences, dat.a1$NbSequences)
+ri<-range(dat$NbSites, dat.a1$NbSites)
+rt<-range(dat$Iteration, dat.a1$Iteration)
+
+par(mar=c(4,4,4,4)+0.1)
+plot(dat$NbSequences~dat$Iteration, type="b", col="black", pch=4, ylim=re, xlim=rt, ylab="# sequences", xlab="iteration", lwd=2)
+lines((dat$NbSites-ri[1])*diff(re)/diff(ri)+re[1]~dat$Iteration, type="b", col="black", pch=1, lwd=2)
+step<-round(diff(ri)/5)
+axis(side = 4, at = seq(re[1], re[2], by=step*diff(re)/diff(ri)), labels = seq(ri[1], ri[2], by=step))
+mtext(side = 4, line = 3, text = "# sites")
+
+lines(dat.a1$NbSequences~dat.a1$Iteration, type="b", col=cols[1], pch=4, lwd=2)
+lines((dat.a1$NbSites-ri[1])*diff(re)/diff(ri)+re[1]~dat.a1$Iteration, type="b", col=cols[1], pch=1, lwd=2)
+
+lines(dat.a2$NbSequences~dat.a2$Iteration, type="b", col=cols[2], pch=4, lwd=2)
+lines((dat.a2$NbSites-ri[1])*diff(re)/diff(ri)+re[1]~dat.a2$Iteration, type="b", col=cols[2], pch=1, lwd=2)
+
+lines(dat.a3$NbSequences~dat.a3$Iteration, type="b", col=cols[3], pch=4, lwd=2)
+lines((dat.a3$NbSites-ri[1])*diff(re)/diff(ri)+re[1]~dat.a3$Iteration, type="b", col=cols[3], pch=1, lwd=2)
+
+lines(dat.a4$NbSequences~dat.a4$Iteration, type="b", col=cols[4], pch=4, lwd=2)
+lines((dat.a4$NbSites-ri[1])*diff(re)/diff(ri)+re[1]~dat.a4$Iteration, type="b", col=cols[4], pch=1, lwd=2)
+
+lines(dat.a5$NbSequences~dat.a5$Iteration, type="b", col=cols[5], pch=4, lwd=2)
+lines((dat.a5$NbSites-ri[1])*diff(re)/diff(ri)+re[1]~dat.a5$Iteration, type="b", col=cols[5], pch=1, lwd=2)
+
+lines(dat.a6$NbSequences~dat.a6$Iteration, type="b", col=cols[6], pch=4, lwd=2)
+lines((dat.a6$NbSites-ri[1])*diff(re)/diff(ri)+re[1]~dat.a6$Iteration, type="b", col=cols[6], pch=1, lwd=2)
+
+# Tradeoff curves:
+myplot<-function(dat, col) {
+ lines(relSit~relSeq, dat, pch=19, col=col, lwd=2, type="b")
+}
+plot(relSit~relSeq, dat, pch=19, col="black", lwd=2, type="b", xlab="% sequences removed", ylab="% site gains", ylim=c(0, 0.4))
+myplot(dat.a1, col=cols[1])
+myplot(dat.a2, col=cols[2])
+myplot(dat.a3, col=cols[3])
+myplot(dat.a4, col=cols[4])
+myplot(dat.a5, col=cols[5])
+myplot(dat.a6, col=cols[6])
+legend(0, 0.4, col=c("black", cols), pch=19, lwd=2, lty="solid", legend=c("FastTree", "complete", "single", "average", "median", "centroid", "Ward"))
+
diff --git a/man/CMakeLists.txt b/man/CMakeLists.txt
new file mode 100644
index 0000000..a9a78e4
--- /dev/null
+++ b/man/CMakeLists.txt
@@ -0,0 +1,7 @@
+# CMake script for the physamp package
+# Author: Julien Dutheil
+# Created: 24/10/2014
+
+IF(MAN)
+ INSTALL(FILES bppalnoptim.1.gz DESTINATION share/man/man1)
+ENDIF(MAN)
diff --git a/man/bppalnoptim.1.txt b/man/bppalnoptim.1.txt
new file mode 100644
index 0000000..a25f666
--- /dev/null
+++ b/man/bppalnoptim.1.txt
@@ -0,0 +1,37 @@
+.TH BPPALNOPTIM 1 LOCAL
+
+.SH NAME
+
+bppalnoptim - Sequence alignment optimization according to the number of sequences vs. number of sites trade-off
+
+.SH SYNOPSIS
+
+.B bppalnoptim [options]
+
+.SH AVAILABILITY
+
+All UNIX flavors
+
+.SH DESCRIPTION
+
+bppalnoptim samples sequences from an alignment in order to maximize the number of sites with a given minimal coverage.
+
+.SH OPTIONS
+
+You should refer to 'info physamp' or to the online manual of physamp for a complete list of available options.
+
+.TP 5
+
+--noninteractive=yes
+
+generates output for redirection into a file.
+
+.TP
+
+param=file
+
+reads a file for loading options
+
+.SH AUTHOR
+
+Julien Dutheil.
diff --git a/physamp/AlignmentOptimizer.cpp b/physamp/AlignmentOptimizer.cpp
new file mode 100755
index 0000000..3c6030f
--- /dev/null
+++ b/physamp/AlignmentOptimizer.cpp
@@ -0,0 +1,775 @@
+//
+// File: bppAlignmentOptimizer.cpp
+// Created by: Julien Dutheil
+// Created on: October 24th 2014 11:15
+//
+
+/*
+ This file is part of the PhySamp package.
+
+ PhySamp 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.
+
+ PhySamp 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
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with Foobar. If not, see <http://www.gnu.org/licenses/>.
+*/
+
+// From the STL:
+#include <iostream>
+#include <iomanip>
+
+using namespace std;
+
+#include <Bpp/App/BppApplication.h>
+#include <Bpp/App/ApplicationTools.h>
+#include <Bpp/Io/FileTools.h>
+#include <Bpp/Text/TextTools.h>
+#include <Bpp/Text/KeyvalTools.h>
+#include <Bpp/Numeric/DataTable.h>
+#include <Bpp/Numeric/Random/RandomTools.h>
+
+// From bpp-seq:
+#include <Bpp/Seq/Alphabet.all>
+#include <Bpp/Seq/Container.all>
+#include <Bpp/Seq/SiteTools.h>
+#include <Bpp/Seq/App/SequenceApplicationTools.h>
+
+// From bpp-phyl:
+#include <Bpp/Phyl/TreeTemplate.h>
+#include <Bpp/Phyl/Distance/HierarchicalClustering.h>
+#include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
+
+using namespace bpp;
+
+void help()
+{
+ (*ApplicationTools::message << "__________________________________________________________________________").endLine();
+ (*ApplicationTools::message << "bppalnoptim parameter1_name=parameter1_value").endLine();
+ (*ApplicationTools::message << " parameter2_name=parameter2_value ... param=option_file").endLine();
+ (*ApplicationTools::message).endLine();
+ (*ApplicationTools::message << " Refer to the Bio++ Program Suite Manual for a list of available options.").endLine();
+ (*ApplicationTools::message << "__________________________________________________________________________").endLine();
+}
+
+//Note: this is too slow!
+double overlapDistance(const Sequence& seq1, const Sequence& seq2) {
+ //double n1 = 0, n2 = 0, n12 = 0;
+ double n12 = 0;
+ const Alphabet* a = seq1.getAlphabet();
+ for (size_t i = 0; i < seq1.size(); ++i) {
+ //if (!a->isGap(seq1[i])) n1++;
+ //if (!a->isGap(seq2[i])) n2++;
+ if (!a->isGap(seq1[i]) && !a->isGap(seq2[i])) n12++;
+ }
+ //return (1. - 2. * n12 / (n1 + n2));
+ return (static_cast<double>(seq1.size()) - n12);
+}
+
+double overlapDistance(const vector<bool>& seq1, const vector<bool>& seq2) {
+ double n12 = 0;
+ for (size_t i = 0; i < seq1.size(); ++i) {
+ if (seq1[i] && seq2[i]) n12++;
+ }
+ return (static_cast<double>(seq1.size()) - n12);
+}
+
+struct Group {
+ public:
+ int id;
+ char direction;
+ unsigned int nbSites;
+ unsigned int nbSequences;
+ unsigned int nbChars;
+
+ public:
+ Group(int nodeId,
+ char dir,
+ unsigned int nsi,
+ unsigned int nse,
+ unsigned int nch):
+ id(nodeId), direction(dir),
+ nbSites(nsi), nbSequences(nse), nbChars(nch)
+ {}
+};
+
+class AlignmentPartitionScores {
+ public:
+ int id; //Needed later when in a vector and not a map
+ unsigned int nbSitesUp;
+ unsigned int nbSitesDown;
+ unsigned int nbSequencesUp;
+ unsigned int nbSequencesDown;
+ unsigned int nbCharsUp;
+ unsigned int nbCharsDown;
+
+ public:
+ AlignmentPartitionScores():
+ id(-1),
+ nbSitesUp(0),
+ nbSitesDown(0),
+ nbSequencesUp(0),
+ nbSequencesDown(0),
+ nbCharsUp(0),
+ nbCharsDown(0)
+ {}
+
+ virtual ~AlignmentPartitionScores() {}
+
+ public:
+ Group getGroupUp() const {
+ return Group(id, 'u', nbSitesUp, nbSequencesUp, nbCharsUp);
+ }
+
+ Group getGroupDown() const {
+ return Group(id, 'd', nbSitesDown, nbSequencesDown, nbCharsDown);
+ }
+};
+
+//Complete site version:
+class AlignmentPartitionScores1:
+ public AlignmentPartitionScores
+{
+ public:
+ vector<bool> up;
+ vector<bool> down;
+
+ public:
+ AlignmentPartitionScores1():
+ up(), down() {}
+ virtual ~AlignmentPartitionScores1() {}
+};
+
+//Version allowing a certain amount of gaps:
+class AlignmentPartitionScores2:
+ public AlignmentPartitionScores
+{
+ public:
+ vector<unsigned int> up;
+ vector<unsigned int> down;
+
+ public:
+ AlignmentPartitionScores2():
+ up(), down() {}
+ virtual ~AlignmentPartitionScores2() {}
+};
+
+class Comparator {
+ private:
+ char method_;
+
+ public:
+ Comparator(char method): method_(method) {}
+
+ public:
+ bool operator() (Group a, Group b) {
+ if (method_ == 'a') {
+ if (a.nbSequences == b.nbSequences) {
+ if (a.nbSites == b.nbSites) {
+ return (a.nbChars > b.nbChars);
+ } else {
+ return (a.nbSites > b.nbSites);
+ }
+ } else {
+ return (a.nbSequences > b.nbSequences);
+ }
+ } else if (method_ == 'b') {
+ return (a.nbChars > b.nbChars);
+ } else {
+ return (true);
+ }
+ }
+
+ bool isImproving(Group& a, size_t nbSites, size_t nbChars) {
+ if (method_ == 'a')
+ return (a.nbSites > nbSites);
+ else if (method_ == 'b') {
+ return (a.nbChars > nbChars);
+ } else {
+ return false;
+ }
+ }
+};
+
+
+#define Index2 map<int, AlignmentPartitionScores2>
+
+// Recursive function.
+// This will initialize the scores map and set the down variables.
+// For convenience, we return the scores for the root subtree.
+AlignmentPartitionScores2& gapOptimizerFirstTreeTraversal2(const Node& node, const SiteContainer& sites, Index2& scores, double threshold, bool filterGaps, bool filterUnresolved, const vector<unsigned int>& reference, size_t nbSequencesRef)
+{
+ AlignmentPartitionScores2& nodeScores = scores[node.getId()]; //This eventually creates scores for this node.
+ size_t nbSites = sites.getNumberOfSites();
+ nodeScores.id = node.getId();
+ nodeScores.down.assign(nbSites, 0);
+ nodeScores.nbSitesDown = 0;
+ nodeScores.nbCharsDown = 0;
+
+ //We distinguish two cases, whether the node is a leaf or an inner node:
+ if (node.isLeaf()) {
+ //This is a leaf, we initialize arrays from the sequence data.
+ const Sequence& seq = sites.getSequence(node.getName()); //We assume that the alignment contains all leaves of the tree.
+ //This one at least is trivial:
+ nodeScores.nbSequencesDown = 1;
+ //Now we need to initialize the bit vector and count sites:
+ for (size_t i = 0; i < nbSites; ++i) {
+ bool test = !((filterGaps && seq.getAlphabet()->isGap(seq[i])) || (filterUnresolved && seq.getAlphabet()->isUnresolved(seq[i])));
+ nodeScores.down[i] += (test ? 1 : 0);
+ }
+ } else {
+ //This is an inner node.
+ //All calculations are performed recursively from the results of son nodes:
+ nodeScores.nbSequencesDown = 0;
+ for (size_t k = 0; k < node.getNumberOfSons(); ++k) {
+ //We loop over all son nodes:
+ const Node* son = node.getSon(k);
+ //We need to make computations for the subtree first and get the results:
+ AlignmentPartitionScores2& sonScores = gapOptimizerFirstTreeTraversal2(*son, sites, scores, threshold, filterGaps, filterUnresolved, reference, nbSequencesRef);
+ //Now we make computations for this node:
+ nodeScores.nbSequencesDown += sonScores.nbSequencesDown;
+ for (size_t i = 0; i < nbSites; ++i)
+ nodeScores.down[i] += sonScores.down[i];
+ }
+ }
+ //Finally we count all sites:
+ for (size_t i = 0; i < nbSites; ++i) {
+ if (static_cast<double>(nodeScores.down[i] + reference[i]) / static_cast<double>(nodeScores.nbSequencesDown + nbSequencesRef) >= threshold) {
+ nodeScores.nbSitesDown++;
+ nodeScores.nbCharsDown += nodeScores.down[i];
+ }
+ }
+ return nodeScores;
+}
+
+// Recursive function.
+// This will initialize the scores map and set the up variables.
+// This must be ran after the first tree traversal, so that all scores are already initialized.
+void gapOptimizerSecondTreeTraversal2(const Node& node, const SiteContainer& sites, Index2& scores, double threshold, const vector<unsigned int>& reference, size_t nbSequencesRef)
+{
+ AlignmentPartitionScores2& nodeScores = scores[node.getId()]; //This was created during the first pass.
+ size_t nbSites = sites.getNumberOfSites();
+ nodeScores.up.assign(nbSites, 0);
+ nodeScores.nbSitesUp = 0;
+ nodeScores.nbCharsUp = 0;
+ if (node.hasFather()) {
+ //If the node is root, there is nothing to do here...
+ const Node* father = node.getFather();
+ AlignmentPartitionScores2& fatherScores = scores[father->getId()];
+ //We initialize the up array to the one of it father:
+ nodeScores.up = fatherScores.up;
+ nodeScores.nbSequencesUp = fatherScores.nbSequencesUp;
+ //No we check all uncle nodes:
+ for (size_t k = 0; k < father->getNumberOfSons(); ++k) {
+ const Node* uncle = father->getSon(k);
+ if (uncle != &node) {
+ AlignmentPartitionScores2& uncleScores = scores[uncle->getId()];
+ nodeScores.nbSequencesUp += uncleScores.nbSequencesDown;
+ for (size_t i = 0; i < nbSites; ++i) {
+ nodeScores.up[i] += uncleScores.down[i];
+ }
+ }
+ }
+ } else {
+ nodeScores.nbSequencesUp = 0;
+ }
+ //Finally we count all sites:
+ for (size_t i = 0; i < nbSites; ++i) {
+ if (static_cast<double>(nodeScores.up[i] + reference[i]) / static_cast<double>(nodeScores.nbSequencesUp + nbSequencesRef) >= threshold) {
+ nodeScores.nbSitesUp++;
+ nodeScores.nbCharsUp += nodeScores.up[i];
+ }
+ }
+
+ // Recursive call on son nodes (this does not do anything for leaves):
+ for (size_t k = 0; k < node.getNumberOfSons(); ++k) {
+ gapOptimizerSecondTreeTraversal2(*node.getSon(k), sites, scores, threshold, reference, nbSequencesRef);
+ }
+}
+
+// Update function.
+void gapOptimizerUpstreamUpdate2(const Node& node, const Node* from, const SiteContainer& sites, Index2& scores, double threshold, const vector<unsigned int>& reference, size_t nbSequencesRef)
+{
+ if (!node.isLeaf()) {
+ size_t nbSites = sites.getNumberOfSites();
+ AlignmentPartitionScores2& nodeScores = scores[node.getId()];
+ nodeScores.down.assign(nbSites, 0);
+ nodeScores.nbSequencesDown = 0;
+ nodeScores.nbSitesDown = 0;
+ nodeScores.nbCharsDown = 0;
+ for (size_t k = 0; k < node.getNumberOfSons(); ++k) {
+ //We loop over all son nodes:
+ const Node* son = node.getSon(k);
+ //We need to make computations for the subtree first and get the results:
+ AlignmentPartitionScores2& sonScores = scores[son->getId()];
+ //Now we make computations for this node:
+ nodeScores.nbSequencesDown += sonScores.nbSequencesDown;
+ for (size_t i = 0; i < nbSites; ++i)
+ nodeScores.down[i] += sonScores.down[i];
+ if (from && son->getId() != from->getId()) {
+ //Now we update all up nodes in uncle nodes:
+ gapOptimizerSecondTreeTraversal2(*son, sites, scores, threshold, reference, nbSequencesRef);
+ }
+ }
+ //Finally we count all sites:
+ for (size_t i = 0; i < nbSites; ++i) {
+ if (static_cast<double>(nodeScores.down[i] + reference[i]) / static_cast<double>(nodeScores.nbSequencesDown + nbSequencesRef) >= threshold) {
+ nodeScores.nbSitesDown++;
+ nodeScores.nbCharsDown += nodeScores.down[i];
+ }
+ }
+ }
+ if (node.hasFather()) gapOptimizerUpstreamUpdate2(*node.getFather(), &node, sites, scores, threshold, reference, nbSequencesRef);
+}
+
+AlignmentPartitionScores2& gapOptimizerDownstreamUpdate2(const Node& node, const SiteContainer& sites, Index2& scores, double threshold, bool filterGaps, bool filterUnresolved, const vector<unsigned int>& reference, size_t nbSequencesRef)
+{
+ AlignmentPartitionScores2& nodeScores = scores[node.getId()]; //This eventually creates scores for this node.
+ size_t nbSites = sites.getNumberOfSites();
+ nodeScores.id = node.getId();
+ nodeScores.down.assign(nbSites, 0);
+ nodeScores.nbSitesDown = 0;
+ nodeScores.nbCharsDown = 0;
+
+ //We distinguish two cases, whether the node is a leaf or an inner node:
+ if (node.isLeaf()) {
+ //This is a leaf, we initialize arrays from the sequence data.
+ const Sequence& seq = sites.getSequence(node.getName()); //We assume that the alignment contains all leaves of the tree.
+ //This one at least is trivial:
+ nodeScores.nbSequencesDown = 1;
+ //Now we need to initialize the bit vector and count sites:
+ for (size_t i = 0; i < nbSites; ++i) {
+ bool test = !((filterGaps && seq.getAlphabet()->isGap(seq[i])) || (filterUnresolved && seq.getAlphabet()->isUnresolved(seq[i])));
+ nodeScores.down[i] = (test ? 1 : 0);
+ }
+ } else {
+ //This is an inner node.
+ //All calculations are performed recursively from the results of son nodes:
+ nodeScores.nbSequencesDown = 0;
+ for (size_t k = 0; k < node.getNumberOfSons(); ++k) {
+ //We loop over all son nodes:
+ const Node* son = node.getSon(k);
+ //We need to make computations for the subtree first and get the results:
+ AlignmentPartitionScores2& sonScores = scores[son->getId()];
+ //Now we make computations for this node:
+ nodeScores.nbSequencesDown += sonScores.nbSequencesDown;
+ for (size_t i = 0; i < nbSites; ++i)
+ nodeScores.down[i] += sonScores.down[i];
+ }
+ }
+ //Finally we count all sites:
+ for (size_t i = 0; i < nbSites; ++i) {
+ if (static_cast<double>(nodeScores.down[i] + reference[i]) / static_cast<double>(nodeScores.nbSequencesDown + nbSequencesRef) >= threshold) {
+ nodeScores.nbSitesDown++;
+ nodeScores.nbCharsDown += nodeScores.down[i];
+ }
+ }
+ return nodeScores;
+}
+
+
+
+class Selector {
+ public:
+ virtual size_t getSelection(size_t nbChoices) const = 0;
+};
+
+class AutoSelector: public Selector {
+ public:
+ virtual size_t getSelection(size_t nbChoices) const { return (nbChoices > 0 ? 1 : 0); }
+};
+
+class InputSelector: public Selector {
+ public:
+ virtual size_t getSelection(size_t nbChoices) const {
+ cout << "Your choice (0 to stop):" << endl;
+ size_t choice;
+ cin >> choice;
+ return choice;
+ }
+};
+
+
+
+int main(int args, char ** argv)
+{
+ cout << "******************************************************************" << endl;
+ cout << "* Bio++ Alignment Optimizer, version 0.2.0. *" << endl;
+ cout << "* Author: J. Dutheil Last Modif. 23/03/15 *" << endl;
+ cout << "* E. Figuet *" << endl;
+ cout << "******************************************************************" << endl;
+ cout << endl;
+
+ if (args == 1)
+ {
+ help();
+ return 0;
+ }
+
+ try {
+
+ BppApplication bppalnoptim(args, argv, "BppAlnOpt");
+ bppalnoptim.startTimer();
+
+ //Get sequences:
+ auto_ptr<Alphabet> alphabet(SequenceApplicationTools::getAlphabet(bppalnoptim.getParams()));
+ auto_ptr<SiteContainer> sites(SequenceApplicationTools::getSiteContainer(alphabet.get(), bppalnoptim.getParams()));
+
+ //Get options:
+ double threshold = ApplicationTools::getDoubleParameter("threshold", bppalnoptim.getParams(), 0.5, "", true, 1);
+ ApplicationTools::displayResult("Minimum amount of data per site", threshold);
+ bool filterGaps = ApplicationTools::getBooleanParameter("filter_gaps", bppalnoptim.getParams(), true, "", true, 1);
+ ApplicationTools::displayBooleanResult("Filter gap characters", filterGaps);
+ bool filterUnresolved = ApplicationTools::getBooleanParameter("filter_unresolved", bppalnoptim.getParams(), false, "", true, 1);
+ ApplicationTools::displayBooleanResult("Filter unresolved characters", filterUnresolved);
+ if (!filterGaps && !filterUnresolved)
+ throw Exception("Error, either gap, unresolved characters or both should be filtered!");
+
+ //Deal with reference alignment, if any.
+ vector<string> refSequencesNames = ApplicationTools::getVectorParameter<string>("reference.sequences", bppalnoptim.getParams(), ',', "", "", true, 1);
+ size_t nbSequencesRef = refSequencesNames.size();
+ ApplicationTools::displayResult("Number of reference sequences", nbSequencesRef);
+ AlignedSequenceContainer refAln(alphabet.get());
+ for (size_t i = 0; i < nbSequencesRef; ++i) {
+ try {
+ auto_ptr<Sequence> seq(sites->removeSequence(refSequencesNames[i]));
+ refAln.addSequence(*seq);
+ } catch(SequenceNotFoundException) {
+ throw Exception("No sequence with name '" + refSequencesNames[i] + "' was found in the input alignment.");
+ }
+ }
+ size_t totalNbSites = sites->getNumberOfSites();
+ ApplicationTools::displayResult("Total number of sequences", sites->getNumberOfSequences());
+ ApplicationTools::displayResult("Total number of sites", totalNbSites);
+ vector<unsigned int> reference(totalNbSites, 0);
+ for (size_t i = 0; i < nbSequencesRef; ++i) {
+ const Sequence& seq = refAln.getSequence(i);
+ for (size_t j = 0; j < totalNbSites; ++j) {
+ if (!((filterGaps && alphabet->isGap(seq[j])) || (filterUnresolved && alphabet->isUnresolved(seq[j]))))
+ reference[j]++;
+ }
+ }
+
+ //Get tree:
+ auto_ptr< TreeTemplate<Node> > tree;
+ auto_ptr< TreeTemplate<Node> > origTree;
+
+ //input or cluster:
+ string inputTree = ApplicationTools::getStringParameter("input.tree.method", bppalnoptim.getParams(), "AutoCluster", "", false, 1);
+ map<string, string> inputTreeParams;
+ string inputTreeName;
+ KeyvalTools::parseProcedure(inputTree, inputTreeName, inputTreeParams);
+ if (inputTreeName == "AutoCluster") {
+ //Compute pairwise distance matrix:
+ size_t n = sites->getNumberOfSequences();
+ size_t ns = sites->getNumberOfSites();
+
+ //First we compress sequences:
+ vector< vector<bool> > cseqs(n);
+ ApplicationTools::displayTask("Compressing sequences", true);
+ for (size_t i = 0; i < n; ++i) {
+ ApplicationTools::displayGauge(i, n - 1);
+ const Sequence& seq = sites->getSequence(i);
+ cseqs[i].resize(ns);
+ for (size_t j = 0; j < ns; ++j)
+ cseqs[i][j] = !alphabet->isGap(seq[j]);
+ }
+ ApplicationTools::displayTaskDone();
+
+ size_t totmem = (sizeof(vector< vector<double> >) + (sizeof(vector<double>) + sizeof(double) * n) * n) / 1024 / 1024;
+ ApplicationTools::displayResult("Memory required to store distances (Mb)", totmem);
+ ApplicationTools::displayTask("Computing pairwise overlap matrix", true);
+ DistanceMatrix d(sites->getSequencesNames());
+ size_t k = 0, m = n * (n - 1) / 2;
+ for (size_t i = 1; i < n; ++i) {
+ d(i, i) = 0.;
+ for (size_t j = 0; j < i; ++j) {
+ k++;
+ ApplicationTools::displayGauge(k, m);
+ d(i, j) = d(j, i) = overlapDistance(cseqs[i], cseqs[j]);
+ }
+ }
+ ApplicationTools::displayTaskDone();
+ //Free mem:
+ cseqs.clear();
+
+ //Now we build a cluster tree:
+ string linkage = ApplicationTools::getStringParameter("linkage", inputTreeParams, "median", "", true, 2);
+ string linkMode = "";
+ if (linkage == "complete") linkMode = HierarchicalClustering::COMPLETE;
+ if (linkage == "single" ) linkMode = HierarchicalClustering::SINGLE;
+ if (linkage == "average" ) linkMode = HierarchicalClustering::AVERAGE;
+ if (linkage == "median" ) linkMode = HierarchicalClustering::MEDIAN;
+ if (linkage == "ward" ) linkMode = HierarchicalClustering::WARD;
+ if (linkage == "centroid") linkMode = HierarchicalClustering::CENTROID;
+ if (linkMode == "") throw Exception("Invalid linkage mode: " + linkage + ".");
+ ApplicationTools::displayResult("Clustering linkage mode", linkage);
+ ApplicationTools::displayTask("Computing cluster tree", true);
+ HierarchicalClustering hclust(linkMode, d, true);
+ tree.reset(hclust.getTree());
+ tree->unroot();
+ ApplicationTools::displayTaskDone();
+ } else if (inputTreeName == "File") {
+ tree.reset(dynamic_cast<TreeTemplate<Node> *>(PhylogeneticsApplicationTools::getTree(bppalnoptim.getParams())));
+ if (tree->isRooted()) {
+ ApplicationTools::displayWarning("Tree has been unrooted.");
+ tree->unroot();
+ }
+ origTree.reset(tree->clone()); //We keep a copy of the original tree
+ for (size_t i = 0; i < nbSequencesRef; ++i) {
+ try {
+ TreeTemplateTools::dropLeaf(*tree, refSequencesNames[i]);
+ } catch(NodeNotFoundException&) {} //Just ignore this, tree does not include ref sequences and that is ok.
+ }
+ } else {
+ throw Exception("Unrecognized tree input method: " + inputTreeName + ".");
+ }
+ //Reorder the alignment according to tree and use sequence storage instead of site storage (more efficient);
+ vector<string> leafNames = tree->getLeavesNames();
+ AlignedSequenceContainer* asc = new AlignedSequenceContainer(alphabet.get());
+ for (size_t i = 0; i < leafNames.size(); ++i) {
+ asc->addSequence(sites->getSequence(leafNames[i]));
+ }
+ sites.reset(asc);
+
+ //The main loop:
+ string logPath = ApplicationTools::getAFilePath("output.log", bppalnoptim.getParams(), false, false, "", true, "bppalnoptim.log", 1);
+ ofstream logfile(logPath.c_str());
+ logfile << "Iteration\tChoice\tNode\tNbSequences\tDiffSequences\tNbSites\tDiffSites\tNbChars\tDiffChars\tMeanEntropy" << endl;
+
+ //Build initial scores. This will be updated after each iteration, if needed.
+ Index2 indexedScores;
+ gapOptimizerFirstTreeTraversal2(*tree->getRootNode(), *sites, indexedScores, threshold, filterGaps, filterUnresolved, reference, nbSequencesRef);
+ gapOptimizerSecondTreeTraversal2(*tree->getRootNode(), *sites, indexedScores, threshold, reference, nbSequencesRef);
+
+ //Choose analysis mode:
+ string methodDesc = ApplicationTools::getStringParameter("method", bppalnoptim.getParams(), "Input(show=10)", "", false, 1);
+ string methodName;
+ map<string, string> methodArgs;
+ KeyvalTools::parseProcedure(methodDesc, methodName, methodArgs);
+
+ //We try to maximize the number of sites while removing the minimum number of sequences
+ size_t nbDisplay = 1;
+ auto_ptr<Selector> selector;
+ unsigned int minNbSequences = 0;
+ unsigned int minNbSitesRequired = static_cast<unsigned int>(sites->getNumberOfSites()) + 1;
+ if (methodName == "Auto" || methodName == "Diagnostic") {
+ selector.reset(new AutoSelector());
+ if (methodName == "Auto") {
+ minNbSequences = ApplicationTools::getParameter<unsigned int>("min_nb_sequences", methodArgs, 0, "", true, 1);
+ if (minNbSequences == 0) {
+ double f = ApplicationTools::getParameter<double>("min_relative_nb_sequences", methodArgs, 0, "", true, 1);
+ minNbSequences = static_cast<unsigned int>(floor(static_cast<double>(nbSequencesRef + sites->getNumberOfSequences()) * f));
+ }
+ minNbSitesRequired = ApplicationTools::getParameter<unsigned int>("min_nb_sites", methodArgs, minNbSitesRequired, "", true, 1);
+ if (minNbSitesRequired == 0) {
+ double f = ApplicationTools::getParameter<double>("min_relative_nb_sites", methodArgs, 1, "", true, 1);
+ minNbSitesRequired = static_cast<unsigned int>(floor(static_cast<double>(sites->getNumberOfSites()) * f));
+ }
+ }
+ } else if (methodName == "Input") {
+ selector.reset(new InputSelector());
+ nbDisplay = ApplicationTools::getParameter<size_t>("show", methodArgs, 10, "", false, 2);
+ } else {
+ throw Exception("Unrecognized selection method: " + methodDesc);
+ }
+ if (minNbSequences > 0)
+ ApplicationTools::displayResult("Minimum number of sequences to keep", minNbSequences);
+ if (minNbSitesRequired <= static_cast<unsigned int>(sites->getNumberOfSites()))
+ ApplicationTools::displayResult("Stop when this number of sites is reached", minNbSitesRequired);
+
+ auto_ptr<Comparator> comp;
+ string compCrit = ApplicationTools::getStringParameter("comparison", bppalnoptim.getParams(), "MaxSites", "", false, 1);
+ if (compCrit == "MaxSites") {
+ comp.reset(new Comparator('a'));
+ } else if (compCrit == "MaxChars") {
+ comp.reset(new Comparator('b'));
+ } else {
+ throw Exception("Unrecognized comparison criterion: " + compCrit);
+ }
+ ApplicationTools::displayResult("Comparison criterion:", compCrit);
+
+ bool test = true;
+ unsigned int iteration = 0;
+ vector<string> removedSequenceNames;
+ double meanE = 0;
+ for (size_t i = 0; i < sites->getNumberOfSites(); ++i) {
+ meanE += SiteTools::variabilityShannon(sites->getSite(i), false);
+ }
+ meanE /= static_cast<double>(sites->getNumberOfSites());
+ logfile << "0\t0\t" << tree->getRootId() << "\t" << indexedScores[tree->getRootId()].nbSequencesDown << "\t0\t" << indexedScores[tree->getRootId()].nbSitesDown << "\t0\t" << indexedScores[tree->getRootId()].nbCharsDown << "\t0\t" << meanE << endl;
+ while (test) {
+ iteration++;
+ unsigned int nbSequences = indexedScores[tree->getRootId()].nbSequencesDown;
+ unsigned int nbSites = indexedScores[tree->getRootId()].nbSitesDown;
+ unsigned int nbChars = indexedScores[tree->getRootId()].nbCharsDown;
+ ApplicationTools::displayResult("Number of sequences in alignment", nbSequences);
+ ApplicationTools::displayResult("Number of sites in alignment", nbSites);
+ ApplicationTools::displayResult("Number of chars in alignment", nbChars);
+
+ //Check if we have enough sites:
+ if (nbSites >= minNbSitesRequired) {
+ test = false;
+ continue;
+ }
+ ApplicationTools::displayResult("Mean site entropy in alignment", meanE);
+
+ //Maximizes the number of sites:
+ //First get all splits which improve the number of sites and meet the stopping condition, if any:
+ vector<Group> improvingGroups;
+ for (Index2::iterator it = indexedScores.begin(); it != indexedScores.end(); ++it) {
+ Group gup = it->second.getGroupUp();
+ if (comp->isImproving(gup, nbSites, nbChars) && gup.nbSequences >= minNbSequences)
+ improvingGroups.push_back(gup);
+ Group gdo = it->second.getGroupDown();
+ if (comp->isImproving(gdo, nbSites, nbChars) && gdo.nbSequences >= minNbSequences)
+ improvingGroups.push_back(gdo);
+ }
+ //Second sort according to number of sequences removed:
+ sort(improvingGroups.begin(), improvingGroups.end(), *comp.get());
+
+ //Show all beneficial splits:
+
+ cout << "Choice\tNode\t#seq\t%seq\t#sites\t%sites\t#chars\t%chars" << endl;
+ size_t nbChoices = nbSequences > 2 ? min(improvingGroups.size(), nbDisplay) : 0;
+ for (size_t i = 0; i < nbChoices; ++i) {
+ Group& group = improvingGroups[i];
+ cout << (i+1) << ")\t" << group.id << "\t" << group.nbSequences << "\t" << (static_cast<double>(group.nbSequences) - static_cast<double>(nbSequences)) << "\t" << group.nbSites << "\t+" << (group.nbSites - nbSites) << "\t" << group.nbChars << "\t" << (static_cast<double>(group.nbChars) - static_cast<double>(nbChars)) << endl;
+ }
+ size_t choice = selector->getSelection(nbChoices);
+
+ if (choice == 0)
+ test = false;
+ else {
+ Group& group = improvingGroups[choice - 1];
+ Node* node = tree->getNode(group.id);
+ Node* father = node->getFather();
+ if (group.direction == 'u') {
+ //Main group is 'Up', 'Down' should be removed...
+ Node* grandFather = 0;
+ if (father->hasFather())
+ grandFather = father->getFather();
+ vector<string> removedLeaves = TreeTemplateTools::getLeavesNames(*node);
+ TreeTemplateTools::dropSubtree(*tree, node);
+ removedSequenceNames.insert(removedSequenceNames.end(), removedLeaves.begin(), removedLeaves.end());
+ VectorSiteContainer* selectedSites = new VectorSiteContainer(sites->getAlphabet());
+ SequenceContainerTools::getSelectedSequences(*sites, tree->getLeavesNames(), *selectedSites);
+ sites.reset(selectedSites);
+ //We need to recompute down scores of all parent nodes up to the root:
+ if (grandFather) {
+ gapOptimizerUpstreamUpdate2(*grandFather, 0, *sites, indexedScores, threshold, reference, nbSequencesRef);
+ gapOptimizerSecondTreeTraversal2(*grandFather, *sites, indexedScores, threshold, reference, nbSequencesRef);
+ } else {
+ //The remove clade was branching at the root
+ if (tree->isRooted()) {
+ tree->unroot(); //The tree may have become artifically rooted as we removed one son node, there may be only two left :(
+ gapOptimizerDownstreamUpdate2(*tree->getRootNode(), *sites, indexedScores, threshold, filterGaps, filterUnresolved, reference, nbSequencesRef);
+ }
+ gapOptimizerSecondTreeTraversal2(*tree->getRootNode(), *sites, indexedScores, threshold, reference, nbSequencesRef);
+ }
+ } else {
+ //Main group is 'Down', 'Up' should be removed...
+ //We set the node as new root node and delete the rest of the tree.
+ father->removeSon(node);
+ vector<string> removedLeaves = TreeTemplateTools::getLeavesNames(*tree->getRootNode());
+ TreeTemplateTools::deleteSubtree(tree->getRootNode());
+ removedSequenceNames.insert(removedSequenceNames.end(), removedLeaves.begin(), removedLeaves.end());
+ tree->setRootNode(node);
+ if (tree->getNumberOfLeaves() > 1) {
+ tree->unroot();
+ node = tree->getRootNode(); //update with actual root node
+ //We need to recompute 'down' scores at this node:
+ AlignmentPartitionScores2& nodeScores = indexedScores[tree->getRootId()];
+ size_t alnSize = sites->getNumberOfSites();
+ nodeScores.down.assign(alnSize, 0);
+ nodeScores.nbSitesDown = 0;
+ nodeScores.nbCharsDown = 0;
+ nodeScores.nbSequencesDown = 0;
+ for (size_t k = 0; k < node->getNumberOfSons(); ++k) {
+ //We loop over all son nodes:
+ const Node* son = node->getSon(k);
+ AlignmentPartitionScores2& sonScores = indexedScores[son->getId()];
+ //Now we make computations for this node:
+ nodeScores.nbSequencesDown += sonScores.nbSequencesDown;
+ for (size_t i = 0; i < alnSize; ++i)
+ nodeScores.down[i] += sonScores.down[i];
+ }
+ //Finally we count all sites:
+ for (size_t i = 0; i < alnSize; ++i) {
+ if (static_cast<double>(nodeScores.down[i]) / static_cast<double>(nodeScores.nbSequencesDown) >= threshold) {
+ nodeScores.nbSitesDown++;
+ nodeScores.nbCharsDown += nodeScores.down[i];
+ }
+ }
+ }
+ VectorSiteContainer* selectedSites = new VectorSiteContainer(sites->getAlphabet());
+ SequenceContainerTools::getSelectedSequences(*sites, tree->getLeavesNames(), *selectedSites);
+ sites.reset(selectedSites);
+ //We recompute up scores only:
+ gapOptimizerSecondTreeTraversal2(*tree->getRootNode(), *sites, indexedScores, threshold, reference, nbSequencesRef);
+ }
+ //We update the index by removing unecessary nodes:
+ vector<int> ids = tree->getNodesId();
+ for (Index2::iterator it = indexedScores.begin(); it != indexedScores.end();) {
+ if (find(ids.begin(), ids.end(), it->first) == ids.end()) {
+ indexedScores.erase(it++);
+ } else {
+ ++it;
+ }
+ }
+
+ //Compute entropy:
+ meanE = 0;
+ for (size_t i = 0; i < sites->getNumberOfSites(); ++i) {
+ meanE += SiteTools::variabilityShannon(sites->getSite(i), false);
+ }
+ meanE /= static_cast<double>(sites->getNumberOfSites());
+
+ //Write to log file:
+ logfile << iteration << "\t" << choice << "\t" << group.id << "\t" << group.nbSequences << "\t" << (static_cast<double>(group.nbSequences) - static_cast<double>(nbSequences)) << "\t" << group.nbSites << "\t+" << (group.nbSites - nbSites) << "\t" << group.nbChars << "\t" << (static_cast<double>(group.nbChars) - static_cast<double>(nbChars)) << "\t" << meanE << endl;
+ }
+ }
+ logfile.close();
+
+ if (methodName != "Diagnostic") {
+ //Write final alignment:
+ if (ApplicationTools::getStringParameter("output.sequence.file", bppalnoptim.getParams(), "none", "", true, 1) != "none") {
+ if (nbSequencesRef > 0) {
+ SequenceContainerTools::append(refAln, *sites.get());
+ SequenceApplicationTools::writeAlignmentFile(refAln, bppalnoptim.getParams());
+ } else {
+ SequenceApplicationTools::writeAlignmentFile(*sites.get(), bppalnoptim.getParams());
+ }
+ }
+
+ //Write final tree:
+ if (origTree.get()) {
+ for (size_t i = 0; i < removedSequenceNames.size(); ++i)
+ TreeTemplateTools::dropLeaf(*origTree, removedSequenceNames[i]);
+ PhylogeneticsApplicationTools::writeTree(*origTree.get(), bppalnoptim.getParams());
+ } else {
+ //Warning! This will not contain the reference sequence names! (and that is ok :) ).
+ PhylogeneticsApplicationTools::writeTree(*tree.get(), bppalnoptim.getParams());
+ }
+ }
+
+ bppalnoptim.done();
+ }
+ catch (exception& e)
+ {
+ cout << endl;
+ cout << "_____________________________________________________" << endl;
+ cout << "ERROR!!!" << endl;
+ cout << e.what() << endl;
+ return 1;
+ }
+
+ return 0;
+}
+
diff --git a/physamp/CMakeLists.txt b/physamp/CMakeLists.txt
new file mode 100644
index 0000000..691a966
--- /dev/null
+++ b/physamp/CMakeLists.txt
@@ -0,0 +1,17 @@
+# CMake script for physamp package
+# Author: Julien Dutheil
+# Created: 24/10/2014
+
+#ADD_EXECUTABLE(bppphysamp PhyloSampler.cpp)
+#TARGET_LINK_LIBRARIES(bppphysamp ${LIBS})
+#SET_TARGET_PROPERTIES(bppphysamp PROPERTIES LINK_SEARCH_END_STATIC ${BUILD_STATIC})
+
+ADD_EXECUTABLE(bppalnoptim AlignmentOptimizer.cpp)
+TARGET_LINK_LIBRARIES(bppalnoptim ${LIBS})
+SET_TARGET_PROPERTIES(bppalnoptim PROPERTIES LINK_SEARCH_END_STATIC ${BUILD_STATIC})
+
+# Install progs
+INSTALL(TARGETS
+ #bppphysamp
+ bppalnoptim
+ DESTINATION bin)
--
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