[med-svn] [Git][med-team/gubbins][upstream] New upstream version 2.3.5
Steffen Möller
gitlab at salsa.debian.org
Fri Dec 20 23:23:38 GMT 2019
Steffen Möller pushed to branch upstream at Debian Med / gubbins
Commits:
490cb88e by Steffen Moeller at 2019-12-20T23:00:10Z
New upstream version 2.3.5
- - - - -
6 changed files:
- .travis.yml
- + CHANGELOG.md
- Dockerfile
- − INSTALL.md
- README.md
- CHANGELOG → obsolete_changelog
Changes:
=====================================
.travis.yml
=====================================
@@ -15,10 +15,15 @@ cache:
- "build"
- "$HOME/.cache/pip"
python:
- - "3.4"
+ - "3.5"
sudo: false
install:
- "source ./install_dependencies.sh"
- - "autoreconf -i"
- - "./configure"
-script: "make check"
+before_script:
+- pip install codecov
+script:
+ - autoreconf -i && ./configure --enable-maintainer-mode CFLAGS='-O0 --coverage' && make && make check
+ - cd python && coverage run setup.py test
+after_success:
+ - bash <(curl -s https://codecov.io/bash)
+ - codecov
=====================================
CHANGELOG.md
=====================================
@@ -0,0 +1,616 @@
+# Change Log
+
+## [Unreleased](https://github.com/sanger-pathogens/gubbins/tree/HEAD)
+
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.3.4...HEAD)
+
+**Implemented enhancements:**
+
+- Retaining recombinant free non-polymorphic sites [\#208](https://github.com/sanger-pathogens/gubbins/issues/208)
+
+**Fixed bugs:**
+
+- Segmentation fault with some input files [\#170](https://github.com/sanger-pathogens/gubbins/issues/170)
+- ltmain.sh should be removed? [\#157](https://github.com/sanger-pathogens/gubbins/issues/157)
+
+**Closed issues:**
+
+- Gubbins not generating final\_tree.tre [\#253](https://github.com/sanger-pathogens/gubbins/issues/253)
+- Can gubbins take the fasta file produced by snp-sites as inputs? [\#250](https://github.com/sanger-pathogens/gubbins/issues/250)
+- rho/theta--\> total recombination events? [\#247](https://github.com/sanger-pathogens/gubbins/issues/247)
+- Gubbins output: internal\_5 / internal\_6 node? [\#246](https://github.com/sanger-pathogens/gubbins/issues/246)
+- recombination\_predictions.gff regions are overlapping and duplicated ? [\#240](https://github.com/sanger-pathogens/gubbins/issues/240)
+- Gubbins crashed, please ensure you have enough free memory [\#239](https://github.com/sanger-pathogens/gubbins/issues/239)
+- GFF file output columns [\#234](https://github.com/sanger-pathogens/gubbins/issues/234)
+- what does "Bases in Recombinations" in the stats file refer to? [\#232](https://github.com/sanger-pathogens/gubbins/issues/232)
+- Make the FTP urls actual hyperlinks [\#229](https://github.com/sanger-pathogens/gubbins/issues/229)
+- Failing test on 2.1.0 [\#177](https://github.com/sanger-pathogens/gubbins/issues/177)
+
+**Merged pull requests:**
+
+- Rename exec in docker [\#260](https://github.com/sanger-pathogens/gubbins/pull/260) ([puethe](https://github.com/puethe))
+- Mark as unmaintained [\#259](https://github.com/sanger-pathogens/gubbins/pull/259) ([puethe](https://github.com/puethe))
+- 627258 codecov [\#244](https://github.com/sanger-pathogens/gubbins/pull/244) ([ssjunnebo](https://github.com/ssjunnebo))
+- Add changelog [\#242](https://github.com/sanger-pathogens/gubbins/pull/242) ([ssjunnebo](https://github.com/ssjunnebo))
+- Rt574328 readme [\#241](https://github.com/sanger-pathogens/gubbins/pull/241) ([ssjunnebo](https://github.com/ssjunnebo))
+- Remove INSTALL file [\#238](https://github.com/sanger-pathogens/gubbins/pull/238) ([ssjunnebo](https://github.com/ssjunnebo))
+- 574328 edit readme [\#237](https://github.com/sanger-pathogens/gubbins/pull/237) ([ssjunnebo](https://github.com/ssjunnebo))
+- update changelog [\#228](https://github.com/sanger-pathogens/gubbins/pull/228) ([puethe](https://github.com/puethe))
+
+## [v2.3.4](https://github.com/sanger-pathogens/gubbins/tree/v2.3.4) (2018-07-30)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.3.3...v2.3.4)
+
+**Merged pull requests:**
+
+- dynamically allocate memory to avoid stack overflow [\#227](https://github.com/sanger-pathogens/gubbins/pull/227) ([puethe](https://github.com/puethe))
+
+## [v2.3.3](https://github.com/sanger-pathogens/gubbins/tree/v2.3.3) (2018-07-26)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.3.2...v2.3.3)
+
+**Closed issues:**
+
+- ' INSTALL' doesn't link to INSTALL.md [\#222](https://github.com/sanger-pathogens/gubbins/issues/222)
+
+**Merged pull requests:**
+
+- Dockerfile independent from debian package [\#226](https://github.com/sanger-pathogens/gubbins/pull/226) ([puethe](https://github.com/puethe))
+- universal link [\#224](https://github.com/sanger-pathogens/gubbins/pull/224) ([puethe](https://github.com/puethe))
+- link to install.md [\#223](https://github.com/sanger-pathogens/gubbins/pull/223) ([puethe](https://github.com/puethe))
+
+## [v2.3.2](https://github.com/sanger-pathogens/gubbins/tree/v2.3.2) (2018-06-15)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.3.1...v2.3.2)
+
+**Implemented enhancements:**
+
+- Direct output to a directory [\#209](https://github.com/sanger-pathogens/gubbins/issues/209)
+
+**Fixed bugs:**
+
+- Warning while parsing tree: non-numeric label N38 for internal node [\#154](https://github.com/sanger-pathogens/gubbins/issues/154)
+
+**Closed issues:**
+
+- Is there minimum sample size to use gubbins? [\#213](https://github.com/sanger-pathogens/gubbins/issues/213)
+- gubbins\_drawer graph [\#212](https://github.com/sanger-pathogens/gubbins/issues/212)
+- Running example files [\#211](https://github.com/sanger-pathogens/gubbins/issues/211)
+- TypeError: reroot\_at\_midpoint\(\) got an unexpected keyword argument 'update\_splits' [\#205](https://github.com/sanger-pathogens/gubbins/issues/205)
+- x [\#204](https://github.com/sanger-pathogens/gubbins/issues/204)
+- Input format is not clear [\#185](https://github.com/sanger-pathogens/gubbins/issues/185)
+- Inconsistencies in branch stats file [\#181](https://github.com/sanger-pathogens/gubbins/issues/181)
+- error while loading shared libraries: libgubbins.so.0 [\#156](https://github.com/sanger-pathogens/gubbins/issues/156)
+
+**Merged pull requests:**
+
+- Replaced the script gubbins\_drawer.py with an empty script displaying… [\#221](https://github.com/sanger-pathogens/gubbins/pull/221) ([puethe](https://github.com/puethe))
+- Link check to lsubunit [\#220](https://github.com/sanger-pathogens/gubbins/pull/220) ([puethe](https://github.com/puethe))
+- corrected typo: 'fastree' -\> 'fasttree' [\#219](https://github.com/sanger-pathogens/gubbins/pull/219) ([puethe](https://github.com/puethe))
+- update instructions for Docker [\#217](https://github.com/sanger-pathogens/gubbins/pull/217) ([ssjunnebo](https://github.com/ssjunnebo))
+- added choices to `--tree\_builder` and other args [\#207](https://github.com/sanger-pathogens/gubbins/pull/207) ([schultzm](https://github.com/schultzm))
+- ignore ltmain.sh for language statistics [\#206](https://github.com/sanger-pathogens/gubbins/pull/206) ([ssjunnebo](https://github.com/ssjunnebo))
+- update manual [\#203](https://github.com/sanger-pathogens/gubbins/pull/203) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.3.1](https://github.com/sanger-pathogens/gubbins/tree/v2.3.1) (2017-09-22)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.3.0...v2.3.1)
+
+**Fixed bugs:**
+
+- gubbins\_drawer.py help improvement [\#183](https://github.com/sanger-pathogens/gubbins/issues/183)
+
+**Merged pull requests:**
+
+- Internal nodes [\#202](https://github.com/sanger-pathogens/gubbins/pull/202) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.3.0](https://github.com/sanger-pathogens/gubbins/tree/v2.3.0) (2017-09-21)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.2.3...v2.3.0)
+
+**Fixed bugs:**
+
+- Some options have default listed twice in --help [\#199](https://github.com/sanger-pathogens/gubbins/issues/199)
+
+**Merged pull requests:**
+
+- Gubbins drawer help text [\#201](https://github.com/sanger-pathogens/gubbins/pull/201) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.2.3](https://github.com/sanger-pathogens/gubbins/tree/v2.2.3) (2017-09-15)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.2.2...v2.2.3)
+
+**Fixed bugs:**
+
+- Error running gubbins\_drawer.py with v. 2.2.0 [\#184](https://github.com/sanger-pathogens/gubbins/issues/184)
+
+**Closed issues:**
+
+- Support raxml-AVX2 if available [\#196](https://github.com/sanger-pathogens/gubbins/issues/196)
+- brew install gubbins errors - no formula for pillow [\#194](https://github.com/sanger-pathogens/gubbins/issues/194)
+- gubbins would not run [\#187](https://github.com/sanger-pathogens/gubbins/issues/187)
+
+**Merged pull requests:**
+
+- Fix default extended help text. [\#200](https://github.com/sanger-pathogens/gubbins/pull/200) ([andrewjpage](https://github.com/andrewjpage))
+- allow for AVX2 [\#197](https://github.com/sanger-pathogens/gubbins/pull/197) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.2.2](https://github.com/sanger-pathogens/gubbins/tree/v2.2.2) (2017-09-04)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.2.1...v2.2.2)
+
+**Closed issues:**
+
+- Forgot to make a 2.2.1 release? [\#195](https://github.com/sanger-pathogens/gubbins/issues/195)
+
+## [v2.2.1](https://github.com/sanger-pathogens/gubbins/tree/v2.2.1) (2017-08-02)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.10...v2.2.1)
+
+**Closed issues:**
+
+- Gubbins - Ns in output alignment [\#192](https://github.com/sanger-pathogens/gubbins/issues/192)
+- from gubbins import common ImportError: cannot import name common [\#191](https://github.com/sanger-pathogens/gubbins/issues/191)
+- Losing taxa? [\#189](https://github.com/sanger-pathogens/gubbins/issues/189)
+
+**Merged pull requests:**
+
+- updated manual [\#193](https://github.com/sanger-pathogens/gubbins/pull/193) ([ssjunnebo](https://github.com/ssjunnebo))
+- Manual in docx format [\#188](https://github.com/sanger-pathogens/gubbins/pull/188) ([ssjunnebo](https://github.com/ssjunnebo))
+- Fixed biopython sub\_features bug [\#186](https://github.com/sanger-pathogens/gubbins/pull/186) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v1.4.10](https://github.com/sanger-pathogens/gubbins/tree/v1.4.10) (2016-10-31)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.2.0...v1.4.10)
+
+**Closed issues:**
+
+- removing identical isolates [\#179](https://github.com/sanger-pathogens/gubbins/issues/179)
+
+## [v2.2.0](https://github.com/sanger-pathogens/gubbins/tree/v2.2.0) (2016-10-31)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.1.0...v2.2.0)
+
+**Closed issues:**
+
+- Linuxbrew installs 1.4.7 still [\#176](https://github.com/sanger-pathogens/gubbins/issues/176)
+- Can't find RAxML in path [\#174](https://github.com/sanger-pathogens/gubbins/issues/174)
+- Source install doesn't install python wrappers [\#173](https://github.com/sanger-pathogens/gubbins/issues/173)
+
+**Merged pull requests:**
+
+- dont filter out identical sequences by default [\#180](https://github.com/sanger-pathogens/gubbins/pull/180) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.1.0](https://github.com/sanger-pathogens/gubbins/tree/v2.1.0) (2016-07-22)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v2.0.0...v2.1.0)
+
+**Fixed bugs:**
+
+- slow fastml [\#167](https://github.com/sanger-pathogens/gubbins/issues/167)
+
+**Merged pull requests:**
+
+- Use GTRCAT by default with RAxML [\#175](https://github.com/sanger-pathogens/gubbins/pull/175) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.0.0](https://github.com/sanger-pathogens/gubbins/tree/v2.0.0) (2016-07-15)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.9...v2.0.0)
+
+**Closed issues:**
+
+- .embl output file not opening in Artemis [\#165](https://github.com/sanger-pathogens/gubbins/issues/165)
+
+**Merged pull requests:**
+
+- Raxml reconstruction [\#172](https://github.com/sanger-pathogens/gubbins/pull/172) ([andrewjpage](https://github.com/andrewjpage))
+- Raxml reconstruction [\#171](https://github.com/sanger-pathogens/gubbins/pull/171) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.4.9](https://github.com/sanger-pathogens/gubbins/tree/v1.4.9) (2016-04-15)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.8...v1.4.9)
+
+**Merged pull requests:**
+
+- Duplicate sequences [\#166](https://github.com/sanger-pathogens/gubbins/pull/166) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.4.8](https://github.com/sanger-pathogens/gubbins/tree/v1.4.8) (2016-04-13)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.7...v1.4.8)
+
+**Closed issues:**
+
+- numpy issues [\#159](https://github.com/sanger-pathogens/gubbins/issues/159)
+
+**Merged pull requests:**
+
+- Convert the proc output from bytes to strings [\#164](https://github.com/sanger-pathogens/gubbins/pull/164) ([aaronk](https://github.com/aaronk))
+
+## [v1.4.7](https://github.com/sanger-pathogens/gubbins/tree/v1.4.7) (2016-02-29)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.6...v1.4.7)
+
+**Merged pull requests:**
+
+- midpoint rerooting by default [\#163](https://github.com/sanger-pathogens/gubbins/pull/163) ([andrewjpage](https://github.com/andrewjpage))
+- Fix allocation from stack bug. [\#161](https://github.com/sanger-pathogens/gubbins/pull/161) ([jeromekelleher](https://github.com/jeromekelleher))
+
+## [v1.4.6](https://github.com/sanger-pathogens/gubbins/tree/v1.4.6) (2016-02-29)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.5...v1.4.6)
+
+## [v1.4.5](https://github.com/sanger-pathogens/gubbins/tree/v1.4.5) (2016-01-13)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v.1.4.5...v1.4.5)
+
+## [v.1.4.5](https://github.com/sanger-pathogens/gubbins/tree/v.1.4.5) (2016-01-13)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.4...v.1.4.5)
+
+**Merged pull requests:**
+
+- remove install-sh [\#160](https://github.com/sanger-pathogens/gubbins/pull/160) ([andrewjpage](https://github.com/andrewjpage))
+- Debian bug 807150 [\#158](https://github.com/sanger-pathogens/gubbins/pull/158) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.4.4](https://github.com/sanger-pathogens/gubbins/tree/v1.4.4) (2015-12-09)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.3...v1.4.4)
+
+## [v1.4.3](https://github.com/sanger-pathogens/gubbins/tree/v1.4.3) (2015-11-19)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.2...v1.4.3)
+
+**Closed issues:**
+
+- multithreading [\#151](https://github.com/sanger-pathogens/gubbins/issues/151)
+
+## [v1.4.2](https://github.com/sanger-pathogens/gubbins/tree/v1.4.2) (2015-09-02)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.1...v1.4.2)
+
+**Merged pull requests:**
+
+- check for input files which are too long [\#153](https://github.com/sanger-pathogens/gubbins/pull/153) ([andrewjpage](https://github.com/andrewjpage))
+- update install docs [\#150](https://github.com/sanger-pathogens/gubbins/pull/150) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.4.1](https://github.com/sanger-pathogens/gubbins/tree/v1.4.1) (2015-07-07)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.4.0...v1.4.1)
+
+## [v1.4.0](https://github.com/sanger-pathogens/gubbins/tree/v1.4.0) (2015-07-01)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.3.4...v1.4.0)
+
+**Closed issues:**
+
+- "Binary package - For 64 bit Linux" links to nowhere [\#142](https://github.com/sanger-pathogens/gubbins/issues/142)
+- INSTALL file not obvious [\#129](https://github.com/sanger-pathogens/gubbins/issues/129)
+- segmentation fault [\#49](https://github.com/sanger-pathogens/gubbins/issues/49)
+
+**Merged pull requests:**
+
+- Convert python to 3 [\#149](https://github.com/sanger-pathogens/gubbins/pull/149) ([andrewjpage](https://github.com/andrewjpage))
+- update raxml version for travis [\#148](https://github.com/sanger-pathogens/gubbins/pull/148) ([andrewjpage](https://github.com/andrewjpage))
+- Add build status to README [\#147](https://github.com/sanger-pathogens/gubbins/pull/147) ([bewt85](https://github.com/bewt85))
+- Add TravisCI support [\#146](https://github.com/sanger-pathogens/gubbins/pull/146) ([bewt85](https://github.com/bewt85))
+- Reference URL updated to final published version not early access [\#145](https://github.com/sanger-pathogens/gubbins/pull/145) ([aslett1](https://github.com/aslett1))
+- Manually merge Aidan Delaneys pull request [\#144](https://github.com/sanger-pathogens/gubbins/pull/144) ([andrewjpage](https://github.com/andrewjpage))
+- Detect blocks at end of sequence [\#143](https://github.com/sanger-pathogens/gubbins/pull/143) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.3.4](https://github.com/sanger-pathogens/gubbins/tree/v1.3.4) (2015-05-18)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.3.3...v1.3.4)
+
+**Closed issues:**
+
+- No ./configure in github - need to run autoconf? [\#130](https://github.com/sanger-pathogens/gubbins/issues/130)
+
+## [v1.3.3](https://github.com/sanger-pathogens/gubbins/tree/v1.3.3) (2015-04-16)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.3.1...v1.3.3)
+
+**Merged pull requests:**
+
+- Window size self error [\#140](https://github.com/sanger-pathogens/gubbins/pull/140) ([andrewjpage](https://github.com/andrewjpage))
+- Window size self error [\#139](https://github.com/sanger-pathogens/gubbins/pull/139) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.3.1](https://github.com/sanger-pathogens/gubbins/tree/v1.3.1) (2015-04-16)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.3.0...v1.3.1)
+
+**Merged pull requests:**
+
+- version 1.3.1 [\#138](https://github.com/sanger-pathogens/gubbins/pull/138) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.3.0](https://github.com/sanger-pathogens/gubbins/tree/v1.3.0) (2015-04-16)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.2.4...v1.3.0)
+
+**Merged pull requests:**
+
+- Recalculate genome length [\#137](https://github.com/sanger-pathogens/gubbins/pull/137) ([andrewjpage](https://github.com/andrewjpage))
+- Downstream recombinations [\#136](https://github.com/sanger-pathogens/gubbins/pull/136) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.2.4](https://github.com/sanger-pathogens/gubbins/tree/v1.2.4) (2015-03-31)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.2.3...v1.2.4)
+
+**Merged pull requests:**
+
+- output version in python script [\#135](https://github.com/sanger-pathogens/gubbins/pull/135) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.2.3](https://github.com/sanger-pathogens/gubbins/tree/v1.2.3) (2015-03-30)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.2.2...v1.2.3)
+
+**Merged pull requests:**
+
+- include last element of array [\#134](https://github.com/sanger-pathogens/gubbins/pull/134) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.2.2](https://github.com/sanger-pathogens/gubbins/tree/v1.2.2) (2015-03-30)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.2.1...v1.2.2)
+
+## [v1.2.1](https://github.com/sanger-pathogens/gubbins/tree/v1.2.1) (2015-03-30)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.2.0...v1.2.1)
+
+**Merged pull requests:**
+
+- Correct vcf format and EMBL format [\#133](https://github.com/sanger-pathogens/gubbins/pull/133) ([andrewjpage](https://github.com/andrewjpage))
+- debian changelog [\#132](https://github.com/sanger-pathogens/gubbins/pull/132) ([andrewjpage](https://github.com/andrewjpage))
+- Dont fill in gaps in parent with bases from child [\#131](https://github.com/sanger-pathogens/gubbins/pull/131) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.2.0](https://github.com/sanger-pathogens/gubbins/tree/v1.2.0) (2015-03-06)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.1.2...v1.2.0)
+
+## [v1.1.2](https://github.com/sanger-pathogens/gubbins/tree/v1.1.2) (2015-03-06)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.1.1...v1.1.2)
+
+**Merged pull requests:**
+
+- Update robustness [\#128](https://github.com/sanger-pathogens/gubbins/pull/128) ([andrewjpage](https://github.com/andrewjpage))
+- message about invalid outgroups [\#127](https://github.com/sanger-pathogens/gubbins/pull/127) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.1.1](https://github.com/sanger-pathogens/gubbins/tree/v1.1.1) (2015-01-23)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.1.0...v1.1.1)
+
+**Merged pull requests:**
+
+- Clade as outgroup [\#126](https://github.com/sanger-pathogens/gubbins/pull/126) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.1.0](https://github.com/sanger-pathogens/gubbins/tree/v1.1.0) (2015-01-23)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.12...v1.1.0)
+
+## [v1.0.12](https://github.com/sanger-pathogens/gubbins/tree/v1.0.12) (2015-01-20)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.11...v1.0.12)
+
+**Merged pull requests:**
+
+- test data [\#125](https://github.com/sanger-pathogens/gubbins/pull/125) ([andrewjpage](https://github.com/andrewjpage))
+- Remove internal nodes from final tree [\#124](https://github.com/sanger-pathogens/gubbins/pull/124) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.0.11](https://github.com/sanger-pathogens/gubbins/tree/v1.0.11) (2015-01-19)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.10...v1.0.11)
+
+**Merged pull requests:**
+
+- check fasta files valid and check for intermediate raxml files [\#123](https://github.com/sanger-pathogens/gubbins/pull/123) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.0.10](https://github.com/sanger-pathogens/gubbins/tree/v1.0.10) (2015-01-19)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.9...v1.0.10)
+
+## [v1.0.9](https://github.com/sanger-pathogens/gubbins/tree/v1.0.9) (2015-01-06)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/1.0.9...v1.0.9)
+
+## [1.0.9](https://github.com/sanger-pathogens/gubbins/tree/1.0.9) (2015-01-06)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.8...1.0.9)
+
+**Merged pull requests:**
+
+- Dont use cpu info to find the flags [\#122](https://github.com/sanger-pathogens/gubbins/pull/122) ([andrewjpage](https://github.com/andrewjpage))
+- class namespace [\#121](https://github.com/sanger-pathogens/gubbins/pull/121) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.0.8](https://github.com/sanger-pathogens/gubbins/tree/v1.0.8) (2014-12-08)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.7...v1.0.8)
+
+**Merged pull requests:**
+
+- reduced functionality but more stable cpu info lookup [\#120](https://github.com/sanger-pathogens/gubbins/pull/120) ([andrewjpage](https://github.com/andrewjpage))
+- Rho theta [\#119](https://github.com/sanger-pathogens/gubbins/pull/119) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.0.7](https://github.com/sanger-pathogens/gubbins/tree/v1.0.7) (2014-12-08)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.6...v1.0.7)
+
+**Merged pull requests:**
+
+- allow for variation and exclude zero track length [\#118](https://github.com/sanger-pathogens/gubbins/pull/118) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.0.6](https://github.com/sanger-pathogens/gubbins/tree/v1.0.6) (2014-12-03)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.5...v1.0.6)
+
+## [v1.0.5](https://github.com/sanger-pathogens/gubbins/tree/v1.0.5) (2014-11-19)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.2...v1.0.5)
+
+**Merged pull requests:**
+
+- fasttree executables with titlecase and lowercase [\#117](https://github.com/sanger-pathogens/gubbins/pull/117) ([andrewjpage](https://github.com/andrewjpage))
+- warning message when changing number of threads [\#116](https://github.com/sanger-pathogens/gubbins/pull/116) ([andrewjpage](https://github.com/andrewjpage))
+- Change raxml exec search order [\#115](https://github.com/sanger-pathogens/gubbins/pull/115) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.0.2](https://github.com/sanger-pathogens/gubbins/tree/v1.0.2) (2014-10-16)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0.1...v1.0.2)
+
+**Merged pull requests:**
+
+- rename convergence methods and allow for more [\#114](https://github.com/sanger-pathogens/gubbins/pull/114) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.0.1](https://github.com/sanger-pathogens/gubbins/tree/v1.0.1) (2014-10-14)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v1.0...v1.0.1)
+
+**Merged pull requests:**
+
+- unstable test fixed [\#113](https://github.com/sanger-pathogens/gubbins/pull/113) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v1.0](https://github.com/sanger-pathogens/gubbins/tree/v1.0) (2014-10-14)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/0.6...v1.0)
+
+**Merged pull requests:**
+
+- Converging recombinations [\#112](https://github.com/sanger-pathogens/gubbins/pull/112) ([andrewjpage](https://github.com/andrewjpage))
+
+## [0.6](https://github.com/sanger-pathogens/gubbins/tree/0.6) (2014-09-24)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/0.7...0.6)
+
+## [0.7](https://github.com/sanger-pathogens/gubbins/tree/0.7) (2014-09-24)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v0.6...0.7)
+
+## [v0.6](https://github.com/sanger-pathogens/gubbins/tree/v0.6) (2014-09-09)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v0.5...v0.6)
+
+**Merged pull requests:**
+
+- Gubbins drawer can use recombination embl file [\#111](https://github.com/sanger-pathogens/gubbins/pull/111) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v0.5](https://github.com/sanger-pathogens/gubbins/tree/v0.5) (2014-09-09)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v0.4.1...v0.5)
+
+**Merged pull requests:**
+
+- thread support for raxml [\#110](https://github.com/sanger-pathogens/gubbins/pull/110) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v0.4.1](https://github.com/sanger-pathogens/gubbins/tree/v0.4.1) (2014-09-08)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v0.4...v0.4.1)
+
+**Merged pull requests:**
+
+- Check for lowercase fasttree exec [\#109](https://github.com/sanger-pathogens/gubbins/pull/109) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v0.4](https://github.com/sanger-pathogens/gubbins/tree/v0.4) (2014-09-05)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/v0.3...v0.4)
+
+**Merged pull requests:**
+
+- pairwise rename output files [\#108](https://github.com/sanger-pathogens/gubbins/pull/108) ([andrewjpage](https://github.com/andrewjpage))
+- Update stats headers [\#107](https://github.com/sanger-pathogens/gubbins/pull/107) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v0.3](https://github.com/sanger-pathogens/gubbins/tree/v0.3) (2014-09-04)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/0.2...v0.3)
+
+## [0.2](https://github.com/sanger-pathogens/gubbins/tree/0.2) (2014-09-02)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/0.1.11...0.2)
+
+**Merged pull requests:**
+
+- Catch too few sequences [\#106](https://github.com/sanger-pathogens/gubbins/pull/106) ([andrewjpage](https://github.com/andrewjpage))
+
+## [0.1.11](https://github.com/sanger-pathogens/gubbins/tree/0.1.11) (2014-08-22)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/0.1.10...0.1.11)
+
+**Merged pull requests:**
+
+- version in configure [\#105](https://github.com/sanger-pathogens/gubbins/pull/105) ([andrewjpage](https://github.com/andrewjpage))
+- Support for bipartition trees as input [\#104](https://github.com/sanger-pathogens/gubbins/pull/104) ([andrewjpage](https://github.com/andrewjpage))
+
+## [0.1.10](https://github.com/sanger-pathogens/gubbins/tree/0.1.10) (2014-08-22)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/0.1.9...0.1.10)
+
+**Merged pull requests:**
+
+- print list of excluded sequences [\#103](https://github.com/sanger-pathogens/gubbins/pull/103) ([andrewjpage](https://github.com/andrewjpage))
+
+## [0.1.9](https://github.com/sanger-pathogens/gubbins/tree/0.1.9) (2014-08-22)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/0.1.8...0.1.9)
+
+**Merged pull requests:**
+
+- print errors for invalid input files [\#102](https://github.com/sanger-pathogens/gubbins/pull/102) ([andrewjpage](https://github.com/andrewjpage))
+
+## [0.1.8](https://github.com/sanger-pathogens/gubbins/tree/0.1.8) (2014-08-15)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/0.1.7...0.1.8)
+
+**Merged pull requests:**
+
+- Fasttree exec [\#101](https://github.com/sanger-pathogens/gubbins/pull/101) ([andrewjpage](https://github.com/andrewjpage))
+
+## [0.1.7](https://github.com/sanger-pathogens/gubbins/tree/0.1.7) (2014-08-14)
+[Full Changelog](https://github.com/sanger-pathogens/gubbins/compare/0.1.6...0.1.7)
+
+**Merged pull requests:**
+
+- Build for trusty [\#100](https://github.com/sanger-pathogens/gubbins/pull/100) ([andrewjpage](https://github.com/andrewjpage))
+
+## [0.1.6](https://github.com/sanger-pathogens/gubbins/tree/0.1.6) (2014-08-12)
+**Merged pull requests:**
+
+- Changes from Aidan Delaney [\#99](https://github.com/sanger-pathogens/gubbins/pull/99) ([andrewjpage](https://github.com/andrewjpage))
+- Stats missing snps [\#98](https://github.com/sanger-pathogens/gubbins/pull/98) ([andrewjpage](https://github.com/andrewjpage))
+- update no support option in fastml [\#97](https://github.com/sanger-pathogens/gubbins/pull/97) ([andrewjpage](https://github.com/andrewjpage))
+- move blocks inwards [\#96](https://github.com/sanger-pathogens/gubbins/pull/96) ([andrewjpage](https://github.com/andrewjpage))
+- define is starting tree method as static [\#95](https://github.com/sanger-pathogens/gubbins/pull/95) ([andrewjpage](https://github.com/andrewjpage))
+- starting tree needed to come from args [\#94](https://github.com/sanger-pathogens/gubbins/pull/94) ([andrewjpage](https://github.com/andrewjpage))
+- Python tests [\#93](https://github.com/sanger-pathogens/gubbins/pull/93) ([andrewjpage](https://github.com/andrewjpage))
+- remove duplicate move [\#92](https://github.com/sanger-pathogens/gubbins/pull/92) ([andrewjpage](https://github.com/andrewjpage))
+- dont move in twice [\#91](https://github.com/sanger-pathogens/gubbins/pull/91) ([andrewjpage](https://github.com/andrewjpage))
+- typo in method, too many args [\#90](https://github.com/sanger-pathogens/gubbins/pull/90) ([andrewjpage](https://github.com/andrewjpage))
+- move end block in correct number of snps [\#89](https://github.com/sanger-pathogens/gubbins/pull/89) ([andrewjpage](https://github.com/andrewjpage))
+- Span gaps [\#88](https://github.com/sanger-pathogens/gubbins/pull/88) ([andrewjpage](https://github.com/andrewjpage))
+- translate snps and gaps to original genome space coords [\#87](https://github.com/sanger-pathogens/gubbins/pull/87) ([andrewjpage](https://github.com/andrewjpage))
+- extend blocks over gaps [\#86](https://github.com/sanger-pathogens/gubbins/pull/86) ([andrewjpage](https://github.com/andrewjpage))
+- dont call methods and variables the same thing [\#85](https://github.com/sanger-pathogens/gubbins/pull/85) ([andrewjpage](https://github.com/andrewjpage))
+- remove latest tree symlink if it exists, even if its broken [\#84](https://github.com/sanger-pathogens/gubbins/pull/84) ([andrewjpage](https://github.com/andrewjpage))
+- delete intermediate raxml files [\#83](https://github.com/sanger-pathogens/gubbins/pull/83) ([andrewjpage](https://github.com/andrewjpage))
+- Eliminate memory leaks and uninitalised reads/writes [\#82](https://github.com/sanger-pathogens/gubbins/pull/82) ([andrewjpage](https://github.com/andrewjpage))
+- GPL [\#81](https://github.com/sanger-pathogens/gubbins/pull/81) ([andrewjpage](https://github.com/andrewjpage))
+- reduce memory usage and fix seg fault [\#80](https://github.com/sanger-pathogens/gubbins/pull/80) ([andrewjpage](https://github.com/andrewjpage))
+- move math lib linking to end [\#79](https://github.com/sanger-pathogens/gubbins/pull/79) ([andrewjpage](https://github.com/andrewjpage))
+- move zlib linking to end [\#78](https://github.com/sanger-pathogens/gubbins/pull/78) ([andrewjpage](https://github.com/andrewjpage))
+- swap output suppression [\#77](https://github.com/sanger-pathogens/gubbins/pull/77) ([andrewjpage](https://github.com/andrewjpage))
+- memory leaks [\#76](https://github.com/sanger-pathogens/gubbins/pull/76) ([andrewjpage](https://github.com/andrewjpage))
+- update window creation [\#75](https://github.com/sanger-pathogens/gubbins/pull/75) ([andrewjpage](https://github.com/andrewjpage))
+- part4 log10 [\#74](https://github.com/sanger-pathogens/gubbins/pull/74) ([andrewjpage](https://github.com/andrewjpage))
+- Improving likelihood [\#73](https://github.com/sanger-pathogens/gubbins/pull/73) ([andrewjpage](https://github.com/andrewjpage))
+- Improving likelihood [\#72](https://github.com/sanger-pathogens/gubbins/pull/72) ([andrewjpage](https://github.com/andrewjpage))
+- reroot on outgroup should keep internal nodes [\#71](https://github.com/sanger-pathogens/gubbins/pull/71) ([andrewjpage](https://github.com/andrewjpage))
+- Use bases for gaps for internal nodes after fastml [\#70](https://github.com/sanger-pathogens/gubbins/pull/70) ([andrewjpage](https://github.com/andrewjpage))
+- propagate unambiguous bases up the tree [\#69](https://github.com/sanger-pathogens/gubbins/pull/69) ([andrewjpage](https://github.com/andrewjpage))
+- move inwards one at a time, remove gap extending, Bonferroni correction, sliding window 1 [\#68](https://github.com/sanger-pathogens/gubbins/pull/68) ([andrewjpage](https://github.com/andrewjpage))
+- new window shifting method and bug with detecting snps [\#67](https://github.com/sanger-pathogens/gubbins/pull/67) ([andrewjpage](https://github.com/andrewjpage))
+- dont move window past size of genome [\#66](https://github.com/sanger-pathogens/gubbins/pull/66) ([andrewjpage](https://github.com/andrewjpage))
+- move window in to first snp [\#65](https://github.com/sanger-pathogens/gubbins/pull/65) ([andrewjpage](https://github.com/andrewjpage))
+- Updates to coords other minor bugs [\#64](https://github.com/sanger-pathogens/gubbins/pull/64) ([andrewjpage](https://github.com/andrewjpage))
+- sliding window at half minimum window size [\#63](https://github.com/sanger-pathogens/gubbins/pull/63) ([andrewjpage](https://github.com/andrewjpage))
+- swap bases in snp tab file and cleanup filenames [\#62](https://github.com/sanger-pathogens/gubbins/pull/62) ([andrewjpage](https://github.com/andrewjpage))
+- Gaps can be in ref as well as alt [\#61](https://github.com/sanger-pathogens/gubbins/pull/61) ([andrewjpage](https://github.com/andrewjpage))
+- pairwise [\#60](https://github.com/sanger-pathogens/gubbins/pull/60) ([andrewjpage](https://github.com/andrewjpage))
+- remove filtered sequences from starting tree [\#59](https://github.com/sanger-pathogens/gubbins/pull/59) ([andrewjpage](https://github.com/andrewjpage))
+- missing comma [\#58](https://github.com/sanger-pathogens/gubbins/pull/58) ([andrewjpage](https://github.com/andrewjpage))
+- unquote tree nodes for fastml and check if too much is filtered out [\#57](https://github.com/sanger-pathogens/gubbins/pull/57) ([andrewjpage](https://github.com/andrewjpage))
+- update test files [\#56](https://github.com/sanger-pathogens/gubbins/pull/56) ([andrewjpage](https://github.com/andrewjpage))
+- Fastml no gaps [\#55](https://github.com/sanger-pathogens/gubbins/pull/55) ([andrewjpage](https://github.com/andrewjpage))
+- readme [\#54](https://github.com/sanger-pathogens/gubbins/pull/54) ([andrewjpage](https://github.com/andrewjpage))
+- snp branch output and prefiltering aln [\#53](https://github.com/sanger-pathogens/gubbins/pull/53) ([andrewjpage](https://github.com/andrewjpage))
+- make drawer work with empty tracks [\#52](https://github.com/sanger-pathogens/gubbins/pull/52) ([andrewjpage](https://github.com/andrewjpage))
+- strip off input params when testing if exec is in path [\#51](https://github.com/sanger-pathogens/gubbins/pull/51) ([andrewjpage](https://github.com/andrewjpage))
+- Fastml integration [\#50](https://github.com/sanger-pathogens/gubbins/pull/50) ([andrewjpage](https://github.com/andrewjpage))
+- versioning [\#48](https://github.com/sanger-pathogens/gubbins/pull/48) ([andrewjpage](https://github.com/andrewjpage))
+- Cleanup intermediate files [\#47](https://github.com/sanger-pathogens/gubbins/pull/47) ([andrewjpage](https://github.com/andrewjpage))
+- treat N in the same way as gaps when snp searching [\#46](https://github.com/sanger-pathogens/gubbins/pull/46) ([andrewjpage](https://github.com/andrewjpage))
+- Treat N as gap when extending over gaps at block boundries [\#45](https://github.com/sanger-pathogens/gubbins/pull/45) ([andrewjpage](https://github.com/andrewjpage))
+- use same fasttree params in hybrid [\#44](https://github.com/sanger-pathogens/gubbins/pull/44) ([andrewjpage](https://github.com/andrewjpage))
+- vcf coords start from 1 [\#43](https://github.com/sanger-pathogens/gubbins/pull/43) ([andrewjpage](https://github.com/andrewjpage))
+- unquote strings [\#42](https://github.com/sanger-pathogens/gubbins/pull/42) ([andrewjpage](https://github.com/andrewjpage))
+- default preserve underscores to true [\#41](https://github.com/sanger-pathogens/gubbins/pull/41) ([andrewjpage](https://github.com/andrewjpage))
+- preserve underscores [\#40](https://github.com/sanger-pathogens/gubbins/pull/40) ([andrewjpage](https://github.com/andrewjpage))
+- Reroot around edge [\#39](https://github.com/sanger-pathogens/gubbins/pull/39) ([andrewjpage](https://github.com/andrewjpage))
+- remove calls to reading beginnign of line [\#38](https://github.com/sanger-pathogens/gubbins/pull/38) ([andrewjpage](https://github.com/andrewjpage))
+- Read line memory leak [\#37](https://github.com/sanger-pathogens/gubbins/pull/37) ([andrewjpage](https://github.com/andrewjpage))
+- increase read line memory [\#36](https://github.com/sanger-pathogens/gubbins/pull/36) ([andrewjpage](https://github.com/andrewjpage))
+- resize read line buffer [\#35](https://github.com/sanger-pathogens/gubbins/pull/35) ([andrewjpage](https://github.com/andrewjpage))
+- Copyfile [\#34](https://github.com/sanger-pathogens/gubbins/pull/34) ([andrewjpage](https://github.com/andrewjpage))
+- increase read buffer size [\#33](https://github.com/sanger-pathogens/gubbins/pull/33) ([andrewjpage](https://github.com/andrewjpage))
+- semi colon at end of tree [\#32](https://github.com/sanger-pathogens/gubbins/pull/32) ([andrewjpage](https://github.com/andrewjpage))
+- speedup gubbins [\#31](https://github.com/sanger-pathogens/gubbins/pull/31) ([andrewjpage](https://github.com/andrewjpage))
+- scale distances by num snps [\#30](https://github.com/sanger-pathogens/gubbins/pull/30) ([andrewjpage](https://github.com/andrewjpage))
+- providing a starting tree skips first tree building step [\#29](https://github.com/sanger-pathogens/gubbins/pull/29) ([andrewjpage](https://github.com/andrewjpage))
+- calc bases in recombs [\#28](https://github.com/sanger-pathogens/gubbins/pull/28) ([andrewjpage](https://github.com/andrewjpage))
+- improved stats [\#27](https://github.com/sanger-pathogens/gubbins/pull/27) ([andrewjpage](https://github.com/andrewjpage))
+- calc snp stats and parameter to set min snps [\#26](https://github.com/sanger-pathogens/gubbins/pull/26) ([andrewjpage](https://github.com/andrewjpage))
+- Get all gaps [\#25](https://github.com/sanger-pathogens/gubbins/pull/25) ([andrewjpage](https://github.com/andrewjpage))
+- increase window size to 20k [\#24](https://github.com/sanger-pathogens/gubbins/pull/24) ([andrewjpage](https://github.com/andrewjpage))
+- Span gaps [\#23](https://github.com/sanger-pathogens/gubbins/pull/23) ([andrewjpage](https://github.com/andrewjpage))
+- fasttree needs to use output of gubbins [\#22](https://github.com/sanger-pathogens/gubbins/pull/22) ([andrewjpage](https://github.com/andrewjpage))
+- extend blocks over gaps [\#21](https://github.com/sanger-pathogens/gubbins/pull/21) ([andrewjpage](https://github.com/andrewjpage))
+- raxml exec check [\#20](https://github.com/sanger-pathogens/gubbins/pull/20) ([andrewjpage](https://github.com/andrewjpage))
+- Merge blocks straddling gaps [\#19](https://github.com/sanger-pathogens/gubbins/pull/19) ([andrewjpage](https://github.com/andrewjpage))
+- fix remove [\#18](https://github.com/sanger-pathogens/gubbins/pull/18) ([andrewjpage](https://github.com/andrewjpage))
+- speedup phylip file writing second try [\#17](https://github.com/sanger-pathogens/gubbins/pull/17) ([andrewjpage](https://github.com/andrewjpage))
+- speedup phylip file writing [\#16](https://github.com/sanger-pathogens/gubbins/pull/16) ([andrewjpage](https://github.com/andrewjpage))
+- provide alignment filename not full path for fastree [\#15](https://github.com/sanger-pathogens/gubbins/pull/15) ([andrewjpage](https://github.com/andrewjpage))
+- remove hardcoded path to exec [\#14](https://github.com/sanger-pathogens/gubbins/pull/14) ([andrewjpage](https://github.com/andrewjpage))
+- rerun autoreconf [\#13](https://github.com/sanger-pathogens/gubbins/pull/13) ([andrewjpage](https://github.com/andrewjpage))
+- midpoint rerooting and pairwise comparison [\#12](https://github.com/sanger-pathogens/gubbins/pull/12) ([andrewjpage](https://github.com/andrewjpage))
+- Use get opt long [\#11](https://github.com/sanger-pathogens/gubbins/pull/11) ([andrewjpage](https://github.com/andrewjpage))
+- dont point to gubbins in same dir [\#10](https://github.com/sanger-pathogens/gubbins/pull/10) ([andrewjpage](https://github.com/andrewjpage))
+- dont print out rerooted tree to stdout [\#9](https://github.com/sanger-pathogens/gubbins/pull/9) ([andrewjpage](https://github.com/andrewjpage))
+- Hybrid tree building [\#8](https://github.com/sanger-pathogens/gubbins/pull/8) ([andrewjpage](https://github.com/andrewjpage))
+- Rewrite perl as python [\#7](https://github.com/sanger-pathogens/gubbins/pull/7) ([andrewjpage](https://github.com/andrewjpage))
+- send in most recent phylip file to raxml [\#6](https://github.com/sanger-pathogens/gubbins/pull/6) ([andrewjpage](https://github.com/andrewjpage))
+- run gubbins original snp sites [\#5](https://github.com/sanger-pathogens/gubbins/pull/5) ([andrewjpage](https://github.com/andrewjpage))
+- run gubbins with original snp sites [\#4](https://github.com/sanger-pathogens/gubbins/pull/4) ([andrewjpage](https://github.com/andrewjpage))
+- Gubbins overall tests [\#3](https://github.com/sanger-pathogens/gubbins/pull/3) ([andrewjpage](https://github.com/andrewjpage))
+- Fix memory leak and properly remove recombinations [\#2](https://github.com/sanger-pathogens/gubbins/pull/2) ([andrewjpage](https://github.com/andrewjpage))
+- dont ignore internal nodes [\#1](https://github.com/sanger-pathogens/gubbins/pull/1) ([andrewjpage](https://github.com/andrewjpage))
+
+
+
+\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*
\ No newline at end of file
=====================================
Dockerfile
=====================================
@@ -68,6 +68,3 @@ RUN git clone https://github.com/sanger-pathogens/gubbins.git \
&& make install \
&& cd python \
&& python3 setup.py install
-
-# Rename executable for backwards compatibility
-RUN mv /usr/local/bin/run_gubbins.py /usr/local/bin/run_gubbins
=====================================
INSTALL.md deleted
=====================================
@@ -1,74 +0,0 @@
-Before you do anything, please have a look at the [Gubbins webpage](http://sanger-pathogens.github.io/gubbins/).
-
-# Installation
-There are a few ways to install Gubbins and its dependencies. The simpliest way is using conda.
-
-* OSX/Linux - Bioconda
-* Linux - Ubuntu Xenial (16.04) & Debian (unstable)
-* OSX/Linux/Cloud/Windows - Docker
-* OSX/Linux - from source
-* OSX/Linux/Windows - Virtual Machine
-
-## OSX/Linux - conda
-Install conda and enable the bioconda channels.
-
-```
-conda config --add channels r
-conda config --add channels defaults
-conda config --add channels conda-forge
-conda config --add channels bioconda
-conda install gubbins
-```
-
-## Linux - Ubuntu Xenial (16.04) & Debian (unstable)
-Gubbins has been packaged by the Debian Med team and is trivial to install using apt.
-
- sudo apt-get install gubbins
-
-## OSX/Linux/Cloud/Windows - Docker
-We have a docker container which gets automatically built from the latest version of Gubbins in Debian Med. To install it:
-
- docker pull sangerpathogens/gubbins
-
-To use it you would use a command such as this:
-
- docker run --rm -it -v <local_dir>:<remote_dir> sangerpathogens/gubbins run_gubbins -p <remote_dir>/<prefix> [<options>] <remote_dir>/<alignment_file>
-
-The flag `-v` synchronizes a directory on the host machine (here denoted as `<local_dir>`) with a directory in the Docker container (here denoted as `<remote_dir>`).
-`<remote_dir>` does not need to exist in the container before the run, a common choice is `/data`.
-Note that both `<local_dir>` and `<remote_dir>` must be absolute paths.
-
-The input alignment file must be present in `<local_dir>` (or in one of its subdirectories).
-In order to retrieve the files produced by Gubbins, run the program with option `-p`;
-the argument of this option must consist of `<remote_dir>`, followed by an arbitrary identifier (here denoted as `<prefix>`).
-
-
-## OSX/Linux - from source
-This is the most difficult method and is only suitable for someone with advanced computing skills. Please consider using Conda instead.
-
-Install the dependencies and include them in your `PATH`:
-* [FastTree](http://www.microbesonline.org/fasttree/#Install) ( >=2.1.4 )
-* [RAxML](https://github.com/stamatak/standard-RAxML) ( >=8.0 )
-* Python modules: Biopython (> 1.59), DendroPy (>=4.0), Reportlab, nose, pillow
-* Standard build environment tools (e.g. python3, pip3, make, autoconf, libtool, gcc, check, etc...)
-
-Clone or download the source code from GitHub and run the following commands to install Gubbins:
-```
-autoreconf -i
-./configure [--prefix=$PREFIX]
-make
-[sudo] make install
-cd python
-[sudo] python3 setup.py install
-```
-Use `sudo` to install Gubbins system-wide. If you don't have the permissions, run `configure` with a prefix to install Gubbins in your home directory.
-
-## OSX/Linux/Windows - Virtual Machine
-Roary wont run natively on Windows but we have created a virtual machine which has all of the software setup, along with the test datasets from the paper.
-It is based on [Bio-Linux 8](http://environmentalomics.org/bio-linux/). You need to first install [VirtualBox](https://www.virtualbox.org/),
-then load the virtual machine, using the 'File -> Import Appliance' menu option. The root password is 'manager'.
-
-* ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova
-
-More importantly though, if your trying to do bioinformatics on Windows, your not going to get very far and you should seriously consider upgrading to Linux.
-
=====================================
README.md
=====================================
@@ -1,22 +1,119 @@
-Please see our website for more information on [Gubbins](http://sanger-pathogens.github.io/gubbins/) or read our paper:
+# Gubbins
+Genealogies Unbiased By recomBinations In Nucleotide Sequences
+
+PLEASE NOTE: we currently do not have the resources to provide support for Gubbins, so please do not expect a reply if you flag any issue.
+
+[](http://unmaintained.tech/)
+[](https://travis-ci.org/sanger-pathogens/gubbins)
+[](https://github.com/sanger-pathogens/gubbins/blob/master/LICENSE)
+[](https://academic.oup.com/nar/article/43/3/e15/2410982)
+[](http://bioconda.github.io/recipes/gubbins/README.html)
+[](https://quay.io/repository/biocontainers/gubbins)
+[](https://hub.docker.com/r/sangerpathogens/gubbins)
+[](https://hub.docker.com/r/sangerpathogens/gubbins)
+[](https://codecov.io/gh/sanger-pathogens/gubbins)
+
+
+## Contents
+ * [Introduction](#introduction)
+ * [Installation](#installation)
+ * [Required dependencies](#required-dependencies)
+ * [OSX/Linux \- conda](#osxlinux---conda)
+ * [Linux \- Ubuntu Xenial (16\.04) & Debian (unstable)](#linux---ubuntu-xenial-1604--debian-unstable)
+ * [OSX/Linux/Cloud/Windows \- Docker](#osxlinuxcloudwindows---docker)
+ * [OSX/Linux \- from source](#osxlinux---from-source)
+ * [OSX/Linux/Windows \- Virtual Machine](#osxlinuxwindows---virtual-machine)
+ * [Running the tests](#running-the-tests)
+ * [Usage](#usage)
+ * [Generating Input files](#generating-input-files)
+ * [Output files](#output-files)
+ * [License](#license)
+ * [Feedback/Issues](#feedbackissues)
+ * [Citation](#citation)
+ * [Further Information](#further-information)
+ * [Data from the paper](#data-from-the-paper)
+ * [Midpoint rerooting](#midpoint-rerooting)
+ * [Ancestral sequence reconstruction](#ancestral-sequence-reconstruction)
+
+## Introduction
+Since the introduction of high-throughput, second-generation DNA sequencing technologies, there has been an enormous increase in the size of datasets being used for estimating bacterial population phylodynamics. Although many phylogenetic techniques are scalable to hundreds of bacterial genomes, methods which have been used for mitigating the effect of mechanisms of horizontal sequence transfer on phylogenetic reconstructions cannot cope with these new datasets. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.
-[Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R.
-"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". doi:10.1093/nar/gku1196, Nucleic Acids Research, 2014.]
-(http://nar.oxfordjournals.org/content/43/3/e15)
+## Installation
+Before you do anything, please have a look at the [Gubbins webpage](http://sanger-pathogens.github.io/gubbins/).
-Gubbins
-=======
+### Required dependencies
+* [FastTree](http://www.microbesonline.org/fasttree/#Install) ( >=2.1.4 )
+* [RAxML](https://github.com/stamatak/standard-RAxML) ( >=8.0 )
+* Python modules: Biopython (> 1.59), DendroPy (>=4.0), Reportlab, nose, pillow
+* Standard build environment tools (e.g. python3, pip3, make, autoconf, libtool, gcc, check, etc...)
-[](https://travis-ci.org/sanger-pathogens/gubbins)
+There are a number of ways to install Gubbins and details are provided below. If you encounter an issue when installing Gubbins please contact your local system administrator.
+
+### OSX/Linux - conda
+Install conda and enable the bioconda channels.
+
+```
+conda config --add channels r
+conda config --add channels defaults
+conda config --add channels conda-forge
+conda config --add channels bioconda
+conda install gubbins
+```
+
+### Linux - Ubuntu Xenial (16.04) & Debian (unstable)
+Gubbins has been packaged by the Debian Med team and is trivial to install using apt.
+
+ sudo apt-get install gubbins
+
+### OSX/Linux/Cloud/Windows - Docker
+We have a docker container which gets automatically built from the latest version of Gubbins in Debian Med. To install it:
+
+ docker pull sangerpathogens/gubbins
+
+To use it you would use a command such as this:
+
+ docker run --rm -it -v <local_dir>:<remote_dir> sangerpathogens/gubbins run_gubbins -p <remote_dir>/<prefix> [<options>] <remote_dir>/<alignment_file>
+
+The flag `-v` synchronizes a directory on the host machine (here denoted as `<local_dir>`) with a directory in the Docker container (here denoted as `<remote_dir>`).
+`<remote_dir>` does not need to exist in the container before the run, a common choice is `/data`.
+Note that both `<local_dir>` and `<remote_dir>` must be absolute paths.
+
+The input alignment file must be present in `<local_dir>` (or in one of its subdirectories).
+In order to retrieve the files produced by Gubbins, run the program with option `-p`;
+the argument of this option must consist of `<remote_dir>`, followed by an arbitrary identifier (here denoted as `<prefix>`).
-Since the introduction of high-throughput, second-generation DNA sequencing technologies, there has been an enormous increase in the size of datasets being used for estimating bacterial population phylodynamics. Although many phylogenetic techniques are scalable to hundreds of bacterial genomes, methods which have been used for mitigating the effect of mechanisms of horizontal sequence transfer on phylogenetic reconstructions cannot cope with these new datasets. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.
-Install
-=======
-Please see the [INSTALL](INSTALL.md) file for detailed instructions.
+### OSX/Linux - from source
+This is the most difficult method and is only suitable for someone with advanced computing skills. Please consider using Conda instead.
-Running Gubbins
-===============
+Install the dependencies and include them in your `PATH`.
+
+Clone or download the source code from GitHub and run the following commands to install Gubbins:
+```
+autoreconf -i
+./configure [--prefix=$PREFIX]
+make
+[sudo] make install
+cd python
+[sudo] python3 setup.py install
+```
+Use `sudo` to install Gubbins system-wide. If you don't have the permissions, run `configure` with a prefix to install Gubbins in your home directory.
+
+### OSX/Linux/Windows - Virtual Machine
+Gubbins wont run natively on Windows but we have created a virtual machine which has all of the software setup, along with the test datasets from the paper.
+It is based on [Bio-Linux 8](http://environmentalomics.org/bio-linux/). You need to first install [VirtualBox](https://www.virtualbox.org/),
+then load the virtual machine, using the 'File -> Import Appliance' menu option. The root password is 'manager'.
+
+* ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova
+
+More importantly though, if your trying to do bioinformatics on Windows, your not going to get very far and you should seriously consider upgrading to Linux.
+
+### Running the tests
+The test can be run from the top level directory:
+
+`make check`
+
+## Usage
To run Gubbins with default settings:
run_gubbins.py [FASTA alignment]
@@ -73,17 +170,12 @@ Do not remove files from intermediate iterations. This option will also keep oth
Change the model used by RAxML. The default it GTRCAT (with -V). You can set it to GTRGAMMA.
-Generating Input files
-======================
+### Generating Input files
Any application which can generate a whole genome multi-FASTA alignment can be used with Gubbins, such as [Snippy](https://github.com/tseemann/snippy).
-
-Output files
-==========
-
-Prefix
-------
+### Output files
+__Prefix__
If a prefix is not defined with the –prefix option, the default prefix of the output files is:
X.Y
@@ -91,10 +183,7 @@ where:
X = Prefix taken from the input fasta file
Y = Time stamp. NOTE: This will only be included in the output file prefix if the –u flag has been selected
-
-
-Output file suffices:
----------------------
+__Output file suffices:__
.recombination_predictions.embl
@@ -132,19 +221,28 @@ Final phylogenetic tree in newick format.
Final phylogenetic tree in newick format but with internal node labels.
+## License
+Gubbins is free software, licensed under [GPLv2](https://github.com/sanger-pathogens/gubbins/blob/master/LICENSE).
+
+## Feedback/Issues
+We currently do not have the resources to provide support for Gubbins. However, the community might be able to help you out if you report any issues about usage of the software to the [issues page](https://github.com/sanger-pathogens/gubbins/issues).
+## Citation
+If you use this software please cite:
+[Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R.
+"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". doi:10.1093/nar/gku1196, Nucleic Acids Research, 2014.]
+(http://nar.oxfordjournals.org/content/43/3/e15)
+## Further Information
+For more information on this software see the [Gubbins webpage](http://sanger-pathogens.github.io/gubbins/).
-Data from the paper
-===================
+### Data from the paper
* ftp://ftp.sanger.ac.uk/pub/project/pathogens/gubbins/PMEN1.aln.gz
* ftp://ftp.sanger.ac.uk/pub/project/pathogens/gubbins/ST239.aln.gz
-Midpoint rerooting
-==================
+### Midpoint rerooting
From version 1.3.5 (25/6/15) to version 1.4.6 (29/2/16) trees were not midpoint rerooted by default. This doesnt have any effect on the recombination detection, but the output trees may not look as expected. Users are advised to upgrade to the latest version.
-Ancestral sequence reconstruction
-==================
+### Ancestral sequence reconstruction
From version 2.0.0 onwards, RAxML is used to reconstruction ancestral sequences instead of fastML. RAxML doesnt always produce results as you would expect so the results can be lower quaility than fastML. If you would like to stick with fastML for ancestral sequence reconstruction, please checkout and install v1.4.9.
=====================================
CHANGELOG → obsolete_changelog
=====================================
@@ -1,6 +1,18 @@
-v2.3.2 - 12 Jan 2018
+v2.3.4 - 30 July 2018
+-----
+Dynamically allocate memory of arrays to circumvent segmentation faults,
+which occur on alignments with a large number of SNPs and are due to stack overflow.
+
+v2.3.3 - 26 July 2018
+-----
+Supply a Dockerfile independent from the Debian package.
+
+v2.3.2 - 29 June 2018
-----
Update installation instructions to remove all reference to HomeBrew.
+Improve handling of several arguments that have a fixed set of possible values.
+Fix of test suite.
+Remove gubbins_drawer.
v2.3.1 - 22 Sept 2017
-----
View it on GitLab: https://salsa.debian.org/med-team/gubbins/commit/490cb88e0c973df3eb02e7e7b3d8e71ee1a80f75
--
View it on GitLab: https://salsa.debian.org/med-team/gubbins/commit/490cb88e0c973df3eb02e7e7b3d8e71ee1a80f75
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