[med-svn] [Git][med-team/roary][master] 6 commits: New upstream version 3.13.0+dfsg
Sascha Steinbiss
gitlab at salsa.debian.org
Fri Nov 8 13:58:18 GMT 2019
Sascha Steinbiss pushed to branch master at Debian Med / roary
Commits:
6e9d3e7a by Sascha Steinbiss at 2019-11-08T13:37:05Z
New upstream version 3.13.0+dfsg
- - - - -
df8414a4 by Sascha Steinbiss at 2019-11-08T13:37:05Z
Merge tag 'upstream/3.13.0+dfsg'
Upstream version 3.13.0+dfsg
- - - - -
6fb24fef by Sascha Steinbiss at 2019-11-08T13:37:23Z
new upstream release
- - - - -
c3b22460 by Sascha Steinbiss at 2019-11-08T13:37:54Z
use debhelper 12
- - - - -
479ac3eb by Sascha Steinbiss at 2019-11-08T13:38:14Z
bump Standards-Version
- - - - -
3703d0ad by Sascha Steinbiss at 2019-11-08T13:57:32Z
update source lintian override location and tags
- - - - -
19 changed files:
- .travis.yml
- + CHANGELOG.md
- README.md
- debian/changelog
- debian/compat
- debian/control
- debian/source.lintian-overrides → debian/source/lintian-overrides
- dist.ini
- lib/Bio/Roary/BedFromGFFRole.pm
- lib/Bio/Roary/External/Cdhit.pm
- lib/Bio/Roary/External/CheckTools.pm
- lib/Bio/Roary/ParseGFFAnnotationRole.pm
- lib/Bio/Roary/ReformatInputGFFs.pm
- t/Bio/Roary/ContigsToGeneIDsFromGFF.t
- t/data/example_annotation.gff.proteome.faa.expected
- t/data/locus_tag_gffs/query_1.gff.proteome.faa.expected
- t/data/locus_tag_gffs/query_2.gff.proteome.faa.expected
- t/data/locus_tag_gffs/query_3.gff.proteome.faa.expected
- t/data/overall_gene_presence_absence.csv
Changes:
=====================================
.travis.yml
=====================================
@@ -23,4 +23,10 @@ env:
- PARALLEL_VERSION=20170822
install:
- "source ./install_dependencies.sh"
-script: "ROARY_FULL_TESTS=1 dzil test"
+before_script:
+ - cpanm --quiet --notest Dist::Zilla::App::Command::cover
+ - cpanm --quiet --notest --skip-satisfied Devel::Cover::Report::Codecov
+script:
+ - ROARY_FULL_TESTS=1 dzil test
+after_success:
+ - dzil cover -test -report codecov
\ No newline at end of file
=====================================
CHANGELOG.md
=====================================
@@ -0,0 +1,977 @@
+# Change Log
+
+## [Unreleased](https://github.com/sanger-pathogens/Roary/tree/HEAD)
+
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.12.0...HEAD)
+
+**Implemented enhancements:**
+
+- Feature Request: Clear error message for duplicated file names [\#363](https://github.com/sanger-pathogens/Roary/issues/363)
+
+**Fixed bugs:**
+
+- uninitialized value warning [\#297](https://github.com/sanger-pathogens/Roary/issues/297)
+- Bio::Root::Exception thrown during core genome alignment, missing some sequence in core\_gene\_alignment.aln [\#224](https://github.com/sanger-pathogens/Roary/issues/224)
+
+**Closed issues:**
+
+- Interpretation accessory\_binary\_genes newick [\#429](https://github.com/sanger-pathogens/Roary/issues/429)
+- No gene annotation in gene\_presence\_absence.csv output [\#428](https://github.com/sanger-pathogens/Roary/issues/428)
+- Compilation aborted at pan\_genome\_post\_analysis [\#427](https://github.com/sanger-pathogens/Roary/issues/427)
+- Could not obtain pan\_genome\_sequences [\#426](https://github.com/sanger-pathogens/Roary/issues/426)
+- Pan genome for fungal genomes [\#425](https://github.com/sanger-pathogens/Roary/issues/425)
+- multifasta for all proteins [\#424](https://github.com/sanger-pathogens/Roary/issues/424)
+- roary\_plots.py KeyError: "X" not in index [\#423](https://github.com/sanger-pathogens/Roary/issues/423)
+- Confirm that use of BLAST's `-max\_target\_seqs` is intentional [\#422](https://github.com/sanger-pathogens/Roary/issues/422)
+- query\_pan\_genome 'Cant access file' error \(Non-Working-Directory inputs\) [\#421](https://github.com/sanger-pathogens/Roary/issues/421)
+- How many .gff files does Roary need? [\#419](https://github.com/sanger-pathogens/Roary/issues/419)
+- Installation through Bioconda not working [\#418](https://github.com/sanger-pathogens/Roary/issues/418)
+- Is it possible to run roary without prokka output files? [\#417](https://github.com/sanger-pathogens/Roary/issues/417)
+- Exiting early because number of clusters is too high [\#415](https://github.com/sanger-pathogens/Roary/issues/415)
+- MSG: Got a sequence without letters. Could not guess alphabet? [\#414](https://github.com/sanger-pathogens/Roary/issues/414)
+- Which is the advantage to pre-use prokka to perform analysis using genbank \(.gbk and gbff\) files? [\#412](https://github.com/sanger-pathogens/Roary/issues/412)
+- issues with running and empty files [\#411](https://github.com/sanger-pathogens/Roary/issues/411)
+- MSG: Got a sequence without letters. Could not guess alphabet [\#410](https://github.com/sanger-pathogens/Roary/issues/410)
+- moose.pm issue [\#407](https://github.com/sanger-pathogens/Roary/issues/407)
+- Tutorial data: extract\_proteome\_from\_gff [\#406](https://github.com/sanger-pathogens/Roary/issues/406)
+- Tutorial data: extract\_proteome\_from\_gff [\#403](https://github.com/sanger-pathogens/Roary/issues/403)
+- gene\_presence\_absence.csv incomplete [\#402](https://github.com/sanger-pathogens/Roary/issues/402)
+- Roary including non-protein coding features? [\#398](https://github.com/sanger-pathogens/Roary/issues/398)
+- Question: what programs can be used to visualize embl and dot files? [\#394](https://github.com/sanger-pathogens/Roary/issues/394)
+- Roary Does not terminated successfully [\#388](https://github.com/sanger-pathogens/Roary/issues/388)
+- python: can't open file 'roary\_plots.py': \[Errno 2\] No such file or directory [\#385](https://github.com/sanger-pathogens/Roary/issues/385)
+- Roary does not finish analysis even though cluster job queue returns successful completion [\#383](https://github.com/sanger-pathogens/Roary/issues/383)
+- Genes \(well\) annotated in prokka end up all in different groups?? [\#355](https://github.com/sanger-pathogens/Roary/issues/355)
+- could not determine version of cd-hit [\#322](https://github.com/sanger-pathogens/Roary/issues/322)
+- Use of uninitialized value in require at \(eval 792\) line 1. [\#308](https://github.com/sanger-pathogens/Roary/issues/308)
+- Error: unexpected input in "\_" [\#299](https://github.com/sanger-pathogens/Roary/issues/299)
+- inconsistent referencing of $TMPDIR ? [\#287](https://github.com/sanger-pathogens/Roary/issues/287)
+
+**Merged pull requests:**
+
+- Include tests in README [\#430](https://github.com/sanger-pathogens/Roary/pull/430) ([ssjunnebo](https://github.com/ssjunnebo))
+- 621556 badges [\#420](https://github.com/sanger-pathogens/Roary/pull/420) ([ssjunnebo](https://github.com/ssjunnebo))
+- Update roary\_plots from .ix to .loc [\#416](https://github.com/sanger-pathogens/Roary/pull/416) ([EvdH0](https://github.com/EvdH0))
+- Use only CDS features from GFF [\#400](https://github.com/sanger-pathogens/Roary/pull/400) ([embatty](https://github.com/embatty))
+- also mention Devel::OverloadInfo and Digest::MD5::File as required Perl dependencies [\#397](https://github.com/sanger-pathogens/Roary/pull/397) ([boegel](https://github.com/boegel))
+- Avoid deprecation errors in roary\_plots [\#389](https://github.com/sanger-pathogens/Roary/pull/389) ([mgalardini](https://github.com/mgalardini))
+
+## [v3.12.0](https://github.com/sanger-pathogens/Roary/tree/v3.12.0) (2018-01-23)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.4...v3.12.0)
+
+**Merged pull requests:**
+
+- Reduce min gene size [\#384](https://github.com/sanger-pathogens/Roary/pull/384) ([ssjunnebo](https://github.com/ssjunnebo))
+
+## [v3.11.4](https://github.com/sanger-pathogens/Roary/tree/v3.11.4) (2018-01-16)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.3...v3.11.4)
+
+**Closed issues:**
+
+- Roary seemed to have stopped prematurely; any way to continue the run? [\#380](https://github.com/sanger-pathogens/Roary/issues/380)
+- Getting prank version without the online check [\#377](https://github.com/sanger-pathogens/Roary/issues/377)
+- Kraken version parsing error: [\#376](https://github.com/sanger-pathogens/Roary/issues/376)
+- 3.11.1 failing 2/55 \(3/791\) tests [\#375](https://github.com/sanger-pathogens/Roary/issues/375)
+- Fix for prank version check [\#361](https://github.com/sanger-pathogens/Roary/issues/361)
+- mafft version check still failing - bug in regexp found [\#360](https://github.com/sanger-pathogens/Roary/issues/360)
+- roary -a =\> Use of uninitialized value in concatenation \(.\) [\#270](https://github.com/sanger-pathogens/Roary/issues/270)
+
+**Merged pull requests:**
+
+- Fix dependancy checking option [\#382](https://github.com/sanger-pathogens/Roary/pull/382) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.11.3](https://github.com/sanger-pathogens/Roary/tree/v3.11.3) (2018-01-12)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.2...v3.11.3)
+
+**Merged pull requests:**
+
+- Version fix [\#379](https://github.com/sanger-pathogens/Roary/pull/379) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.11.2](https://github.com/sanger-pathogens/Roary/tree/v3.11.2) (2018-01-12)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.1...v3.11.2)
+
+**Fixed bugs:**
+
+- ExtractProteomeFromGff.t failing tests 3.11.0 [\#373](https://github.com/sanger-pathogens/Roary/issues/373)
+
+**Merged pull requests:**
+
+- fix mafft and kraken version extraction [\#378](https://github.com/sanger-pathogens/Roary/pull/378) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.11.1](https://github.com/sanger-pathogens/Roary/tree/v3.11.1) (2018-01-10)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.0...v3.11.1)
+
+**Closed issues:**
+
+- Sorting in version 3.11.0: uppercase letters first, lowercase second \(non-alphabetical\) [\#371](https://github.com/sanger-pathogens/Roary/issues/371)
+- Genbank input [\#365](https://github.com/sanger-pathogens/Roary/issues/365)
+- not all annotated features are allocated to the clusters [\#359](https://github.com/sanger-pathogens/Roary/issues/359)
+
+**Merged pull requests:**
+
+- Bedtools getfasta format fix [\#374](https://github.com/sanger-pathogens/Roary/pull/374) ([andrewjpage](https://github.com/andrewjpage))
+- Update roary\_plots.py [\#372](https://github.com/sanger-pathogens/Roary/pull/372) ([franz89](https://github.com/franz89))
+- Issue \#363 add check for duplicate basenames [\#370](https://github.com/sanger-pathogens/Roary/pull/370) ([nickp60](https://github.com/nickp60))
+- README.md: Update Guix install instructions. [\#362](https://github.com/sanger-pathogens/Roary/pull/362) ([wwood](https://github.com/wwood))
+
+## [v3.11.0](https://github.com/sanger-pathogens/Roary/tree/v3.11.0) (2017-10-10)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.2...v3.11.0)
+
+**Fixed bugs:**
+
+- Can't get version of kraken, kraken-report or mafft ? [\#312](https://github.com/sanger-pathogens/Roary/issues/312)
+
+**Closed issues:**
+
+- number\_of\_conserved\_genes.Rtab [\#354](https://github.com/sanger-pathogens/Roary/issues/354)
+- \[question\] Should it take this long? [\#352](https://github.com/sanger-pathogens/Roary/issues/352)
+
+**Merged pull requests:**
+
+- change missing gene in core to be dashes rather than Ns [\#358](https://github.com/sanger-pathogens/Roary/pull/358) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.10.2](https://github.com/sanger-pathogens/Roary/tree/v3.10.2) (2017-09-08)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.1...v3.10.2)
+
+**Closed issues:**
+
+- \[version 3.8.0\] Roary crashes at end on perl error message [\#323](https://github.com/sanger-pathogens/Roary/issues/323)
+- Cant open file: \_accessory\_clusters.clstr [\#320](https://github.com/sanger-pathogens/Roary/issues/320)
+
+**Merged pull requests:**
+
+- get kraken version [\#351](https://github.com/sanger-pathogens/Roary/pull/351) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.10.1](https://github.com/sanger-pathogens/Roary/tree/v3.10.1) (2017-09-07)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.0...v3.10.1)
+
+**Implemented enhancements:**
+
+- Auto-detect if input files are GFF or FASTA [\#348](https://github.com/sanger-pathogens/Roary/issues/348)
+- Can "Fixing input GFF files" be parallelized? [\#342](https://github.com/sanger-pathogens/Roary/issues/342)
+
+**Fixed bugs:**
+
+- The GNU General Public License, Version not specified [\#344](https://github.com/sanger-pathogens/Roary/issues/344)
+
+**Closed issues:**
+
+- MSG: The sequence does not appear to be FASTA format \(lacks a descriptor line '\>'\) [\#346](https://github.com/sanger-pathogens/Roary/issues/346)
+
+**Merged pull requests:**
+
+- Improve input file handling [\#350](https://github.com/sanger-pathogens/Roary/pull/350) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.10.0](https://github.com/sanger-pathogens/Roary/tree/v3.10.0) (2017-09-07)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.1...v3.10.0)
+
+**Closed issues:**
+
+- Use of uninitialized value \(Perl\) [\#345](https://github.com/sanger-pathogens/Roary/issues/345)
+- identical .gff file names from different genome, and then issue with mcl groups [\#341](https://github.com/sanger-pathogens/Roary/issues/341)
+- Cant open file: \_clustered.clstr [\#339](https://github.com/sanger-pathogens/Roary/issues/339)
+
+## [v3.9.1](https://github.com/sanger-pathogens/Roary/tree/v3.9.1) (2017-08-22)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.0...v3.9.1)
+
+**Merged pull requests:**
+
+- Optionally allow paralogs in core gene alignment [\#343](https://github.com/sanger-pathogens/Roary/pull/343) ([andrewjpage](https://github.com/andrewjpage))
+- Script to find frequency of unique genes in samples [\#340](https://github.com/sanger-pathogens/Roary/pull/340) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.9.0](https://github.com/sanger-pathogens/Roary/tree/v3.9.0) (2017-08-09)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.2...v3.9.0)
+
+**Closed issues:**
+
+- roary\_plots: pangenome matrix tree does not look like input.newick tree [\#333](https://github.com/sanger-pathogens/Roary/issues/333)
+- use Roary with RAST files [\#332](https://github.com/sanger-pathogens/Roary/issues/332)
+- Roary [\#329](https://github.com/sanger-pathogens/Roary/issues/329)
+- sampling number is 10 in number of genes in pan and core genome [\#319](https://github.com/sanger-pathogens/Roary/issues/319)
+
+**Merged pull requests:**
+
+- Grammar edits [\#327](https://github.com/sanger-pathogens/Roary/pull/327) ([cgreene](https://github.com/cgreene))
+- allow for inflation factor for MCL to be changed [\#326](https://github.com/sanger-pathogens/Roary/pull/326) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.8.2](https://github.com/sanger-pathogens/Roary/tree/v3.8.2) (2017-05-21)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.1...v3.8.2)
+
+## [v3.8.1](https://github.com/sanger-pathogens/Roary/tree/v3.8.1) (2017-05-21)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.0...v3.8.1)
+
+**Closed issues:**
+
+- BLAST Database error [\#321](https://github.com/sanger-pathogens/Roary/issues/321)
+- Results for same input differ always a bit \(summary\_statistics.txt\) [\#318](https://github.com/sanger-pathogens/Roary/issues/318)
+- Error: Couldnt open GFF file [\#314](https://github.com/sanger-pathogens/Roary/issues/314)
+- Help with query\_pan\_genome [\#313](https://github.com/sanger-pathogens/Roary/issues/313)
+
+**Merged pull requests:**
+
+- update email address [\#325](https://github.com/sanger-pathogens/Roary/pull/325) ([ssjunnebo](https://github.com/ssjunnebo))
+- New option to roary\_plots.py [\#317](https://github.com/sanger-pathogens/Roary/pull/317) ([mgalardini](https://github.com/mgalardini))
+
+## [v3.8.0](https://github.com/sanger-pathogens/Roary/tree/v3.8.0) (2017-01-25)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.1...v3.8.0)
+
+**Closed issues:**
+
+- Old version in the master tarball? [\#300](https://github.com/sanger-pathogens/Roary/issues/300)
+- prank is not installed \(Linuxbrew\) [\#294](https://github.com/sanger-pathogens/Roary/issues/294)
+- roary\_plots.py problem [\#292](https://github.com/sanger-pathogens/Roary/issues/292)
+
+**Merged pull requests:**
+
+- Support latest version of blast [\#306](https://github.com/sanger-pathogens/Roary/pull/306) ([andrewjpage](https://github.com/andrewjpage))
+- infgen [\#305](https://github.com/sanger-pathogens/Roary/pull/305) ([andrewjpage](https://github.com/andrewjpage))
+- update from 108 to 118 [\#304](https://github.com/sanger-pathogens/Roary/pull/304) ([andrewjpage](https://github.com/andrewjpage))
+- update usage text for iterative CD-hit [\#301](https://github.com/sanger-pathogens/Roary/pull/301) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.7.1](https://github.com/sanger-pathogens/Roary/tree/v3.7.1) (2016-11-01)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.0...v3.7.1)
+
+**Closed issues:**
+
+- core\_gene\_alignment.aln missing [\#284](https://github.com/sanger-pathogens/Roary/issues/284)
+- Is these results fine to use? [\#282](https://github.com/sanger-pathogens/Roary/issues/282)
+
+**Merged pull requests:**
+
+- fix spelling [\#280](https://github.com/sanger-pathogens/Roary/pull/280) ([satta](https://github.com/satta))
+- dont add POD to end of R scripts [\#279](https://github.com/sanger-pathogens/Roary/pull/279) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.7.0](https://github.com/sanger-pathogens/Roary/tree/v3.7.0) (2016-09-23)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.9...v3.7.0)
+
+## [v3.6.9](https://github.com/sanger-pathogens/Roary/tree/v3.6.9) (2016-09-22)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.8...v3.6.9)
+
+**Implemented enhancements:**
+
+- I have published a Roary homebrew formula [\#208](https://github.com/sanger-pathogens/Roary/issues/208)
+- Getting Roary into Homebrew [\#152](https://github.com/sanger-pathogens/Roary/issues/152)
+
+**Closed issues:**
+
+- roary\_plots.py missing [\#277](https://github.com/sanger-pathogens/Roary/issues/277)
+- Errors when downloaded sequences from NCBI [\#274](https://github.com/sanger-pathogens/Roary/issues/274)
+- Same dataset different results! [\#271](https://github.com/sanger-pathogens/Roary/issues/271)
+- \_clustered.clstr file does not exist, cannot be read [\#250](https://github.com/sanger-pathogens/Roary/issues/250)
+
+**Merged pull requests:**
+
+- Fixed easy-init warnings - 529655 [\#278](https://github.com/sanger-pathogens/Roary/pull/278) ([psweston](https://github.com/psweston))
+- README.md: Add instructions for GNU Guix. [\#273](https://github.com/sanger-pathogens/Roary/pull/273) ([wwood](https://github.com/wwood))
+
+## [v3.6.8](https://github.com/sanger-pathogens/Roary/tree/v3.6.8) (2016-08-02)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.7...v3.6.8)
+
+**Merged pull requests:**
+
+- Allow gene names from gb [\#266](https://github.com/sanger-pathogens/Roary/pull/266) ([andrewjpage](https://github.com/andrewjpage))
+- Missing genes [\#265](https://github.com/sanger-pathogens/Roary/pull/265) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.6.7](https://github.com/sanger-pathogens/Roary/tree/v3.6.7) (2016-07-26)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.6...v3.6.7)
+
+**Fixed bugs:**
+
+- Roary 3.6.5 giving different \(erroneous\) results compared to 3.5.7 and 3.6.1/3.6.3/3.6.4 [\#263](https://github.com/sanger-pathogens/Roary/issues/263)
+- roary R plots don't work on server --- lack of X11 [\#194](https://github.com/sanger-pathogens/Roary/issues/194)
+
+**Closed issues:**
+
+- empty accessory\_binary\_genes.fa file [\#262](https://github.com/sanger-pathogens/Roary/issues/262)
+- a guix package [\#259](https://github.com/sanger-pathogens/Roary/issues/259)
+- create\_pan\_genome\_plots.R - X11 font problem [\#230](https://github.com/sanger-pathogens/Roary/issues/230)
+- Roary not generating pan\_genome\_reference.fa [\#223](https://github.com/sanger-pathogens/Roary/issues/223)
+- Roary not using packaged executables [\#215](https://github.com/sanger-pathogens/Roary/issues/215)
+
+## [v3.6.6](https://github.com/sanger-pathogens/Roary/tree/v3.6.6) (2016-07-25)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.5...v3.6.6)
+
+**Fixed bugs:**
+
+- GFF parsing doesn't match GFF3 specification [\#249](https://github.com/sanger-pathogens/Roary/issues/249)
+
+**Merged pull requests:**
+
+- Fix empty accessory binary [\#264](https://github.com/sanger-pathogens/Roary/pull/264) ([andrewjpage](https://github.com/andrewjpage))
+- change to dist zilla starter bundle [\#261](https://github.com/sanger-pathogens/Roary/pull/261) ([nds](https://github.com/nds))
+
+## [v3.6.5](https://github.com/sanger-pathogens/Roary/tree/v3.6.5) (2016-07-20)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.4...v3.6.5)
+
+**Merged pull requests:**
+
+- allow new format bedtools and dont look for FASTA in GFF [\#260](https://github.com/sanger-pathogens/Roary/pull/260) ([andrewjpage](https://github.com/andrewjpage))
+- catch divide by zero error [\#258](https://github.com/sanger-pathogens/Roary/pull/258) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.6.4](https://github.com/sanger-pathogens/Roary/tree/v3.6.4) (2016-07-06)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.3...v3.6.4)
+
+**Merged pull requests:**
+
+- drop testing for perl 5.10, add 5.24. dzil no longer works below 5.14 [\#257](https://github.com/sanger-pathogens/Roary/pull/257) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.6.3](https://github.com/sanger-pathogens/Roary/tree/v3.6.3) (2016-07-01)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.2...v3.6.3)
+
+**Merged pull requests:**
+
+- Speed up alignments [\#256](https://github.com/sanger-pathogens/Roary/pull/256) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.6.2](https://github.com/sanger-pathogens/Roary/tree/v3.6.2) (2016-05-10)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.1...v3.6.2)
+
+**Implemented enhancements:**
+
+- Prefix utility commands with roary- ? [\#226](https://github.com/sanger-pathogens/Roary/issues/226)
+
+**Merged pull requests:**
+
+- fix bug Can't exec /bin/sh: Argument list too long [\#247](https://github.com/sanger-pathogens/Roary/pull/247) ([duytintruong](https://github.com/duytintruong))
+- get rid of warning message [\#246](https://github.com/sanger-pathogens/Roary/pull/246) ([satta](https://github.com/satta))
+
+## [v3.6.1](https://github.com/sanger-pathogens/Roary/tree/v3.6.1) (2016-04-18)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.0...v3.6.1)
+
+**Fixed bugs:**
+
+- roary\_plots.py generating flawed plots [\#221](https://github.com/sanger-pathogens/Roary/issues/221)
+
+**Closed issues:**
+
+- Core gene file missing error [\#241](https://github.com/sanger-pathogens/Roary/issues/241)
+
+**Merged pull requests:**
+
+- prefix commands with roary [\#244](https://github.com/sanger-pathogens/Roary/pull/244) ([andrewjpage](https://github.com/andrewjpage))
+- More improvements to roary\_plots [\#240](https://github.com/sanger-pathogens/Roary/pull/240) ([mgalardini](https://github.com/mgalardini))
+
+## [v3.6.0](https://github.com/sanger-pathogens/Roary/tree/v3.6.0) (2016-02-23)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.9...v3.6.0)
+
+**Fixed bugs:**
+
+- MSG: Got a sequence without letters. Could not guess alphabet [\#229](https://github.com/sanger-pathogens/Roary/issues/229)
+
+**Closed issues:**
+
+- Roary 3.5.8 works with -i 80 switch, but not with -i 90 or higher with large datasets? [\#234](https://github.com/sanger-pathogens/Roary/issues/234)
+- How to use multiple switches in commandline? [\#232](https://github.com/sanger-pathogens/Roary/issues/232)
+
+**Merged pull requests:**
+
+- Improvements to roary\_plots [\#236](https://github.com/sanger-pathogens/Roary/pull/236) ([mgalardini](https://github.com/mgalardini))
+- Rollback 3 5 8 [\#235](https://github.com/sanger-pathogens/Roary/pull/235) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.5.9](https://github.com/sanger-pathogens/Roary/tree/v3.5.9) (2016-02-17)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.8...v3.5.9)
+
+**Implemented enhancements:**
+
+- What clusters end up in gene accessory\_binary\_genes.fa ? [\#225](https://github.com/sanger-pathogens/Roary/issues/225)
+
+**Closed issues:**
+
+- roary.github.io just prints HELLO [\#233](https://github.com/sanger-pathogens/Roary/issues/233)
+
+**Merged pull requests:**
+
+- Fix minor typo [\#231](https://github.com/sanger-pathogens/Roary/pull/231) ([abremges](https://github.com/abremges))
+
+## [v3.5.8](https://github.com/sanger-pathogens/Roary/tree/v3.5.8) (2016-01-20)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.7...v3.5.8)
+
+**Implemented enhancements:**
+
+- Getting Roary into Debian Med [\#219](https://github.com/sanger-pathogens/Roary/issues/219)
+- Add embl output file mapping location of each core gene in the core genome alignment [\#192](https://github.com/sanger-pathogens/Roary/issues/192)
+
+**Closed issues:**
+
+- Error message: Cannot find the mcxdeblast executable, please ensure its in your PATH [\#217](https://github.com/sanger-pathogens/Roary/issues/217)
+
+**Merged pull requests:**
+
+- Provide full accessory for building binary tree [\#227](https://github.com/sanger-pathogens/Roary/pull/227) ([andrewjpage](https://github.com/andrewjpage))
+- roary\_plots: new fields in roary output must be parsed away [\#222](https://github.com/sanger-pathogens/Roary/pull/222) ([mgalardini](https://github.com/mgalardini))
+- Debian nitpicks [\#220](https://github.com/sanger-pathogens/Roary/pull/220) ([satta](https://github.com/satta))
+- Core alignment header file [\#218](https://github.com/sanger-pathogens/Roary/pull/218) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.5.7](https://github.com/sanger-pathogens/Roary/tree/v3.5.7) (2015-12-17)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.6...v3.5.7)
+
+**Closed issues:**
+
+- Roary not checking tools needed to run [\#214](https://github.com/sanger-pathogens/Roary/issues/214)
+
+**Merged pull requests:**
+
+- Core gene count [\#213](https://github.com/sanger-pathogens/Roary/pull/213) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.5.6](https://github.com/sanger-pathogens/Roary/tree/v3.5.6) (2015-12-01)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.5...v3.5.6)
+
+**Implemented enhancements:**
+
+- Non-issue, FYI regarding my 'roary2svg.pl' script [\#195](https://github.com/sanger-pathogens/Roary/issues/195)
+
+**Merged pull requests:**
+
+- add roary2svg script [\#212](https://github.com/sanger-pathogens/Roary/pull/212) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.5.5](https://github.com/sanger-pathogens/Roary/tree/v3.5.5) (2015-11-26)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.4...v3.5.5)
+
+**Merged pull requests:**
+
+- CD-hit threads limit [\#211](https://github.com/sanger-pathogens/Roary/pull/211) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.5.4](https://github.com/sanger-pathogens/Roary/tree/v3.5.4) (2015-11-26)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.3...v3.5.4)
+
+**Fixed bugs:**
+
+- Use of uninitialized value in require at \(eval ..\) line 1. [\#204](https://github.com/sanger-pathogens/Roary/issues/204)
+- \[bug\] Newick files in 3.5.1 have branch lengths of 0.0 [\#202](https://github.com/sanger-pathogens/Roary/issues/202)
+
+**Merged pull requests:**
+
+- Accessory binary fasta contains all C's fix [\#210](https://github.com/sanger-pathogens/Roary/pull/210) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.5.3](https://github.com/sanger-pathogens/Roary/tree/v3.5.3) (2015-11-26)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.2...v3.5.3)
+
+**Implemented enhancements:**
+
+- Enhancement: roary -a to continue on if other parameters as well [\#207](https://github.com/sanger-pathogens/Roary/issues/207)
+- Make summary\_statistics a TAB/TSV file? [\#193](https://github.com/sanger-pathogens/Roary/issues/193)
+
+**Fixed bugs:**
+
+- roary --version should return 0 not 255 exit code [\#206](https://github.com/sanger-pathogens/Roary/issues/206)
+- Is the roary -a check complete? [\#205](https://github.com/sanger-pathogens/Roary/issues/205)
+
+## [v3.5.2](https://github.com/sanger-pathogens/Roary/tree/v3.5.2) (2015-11-25)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.1...v3.5.2)
+
+**Fixed bugs:**
+
+- Use of uninitialized value in File::Slurper and Encode.pm [\#196](https://github.com/sanger-pathogens/Roary/issues/196)
+
+**Merged pull requests:**
+
+- Improved dependancy checking [\#209](https://github.com/sanger-pathogens/Roary/pull/209) ([andrewjpage](https://github.com/andrewjpage))
+- Lsf update gene alignments [\#201](https://github.com/sanger-pathogens/Roary/pull/201) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.5.1](https://github.com/sanger-pathogens/Roary/tree/v3.5.1) (2015-11-12)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.0...v3.5.1)
+
+**Fixed bugs:**
+
+- Accessory genes newick file contains full path of infividual files [\#200](https://github.com/sanger-pathogens/Roary/issues/200)
+- add optional dependancy from File::Slurper to stop warnings being printed [\#199](https://github.com/sanger-pathogens/Roary/pull/199) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.5.0](https://github.com/sanger-pathogens/Roary/tree/v3.5.0) (2015-11-12)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.3...v3.5.0)
+
+**Merged pull requests:**
+
+- remove path from accessory tree [\#198](https://github.com/sanger-pathogens/Roary/pull/198) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.4.3](https://github.com/sanger-pathogens/Roary/tree/v3.4.3) (2015-11-11)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.2...v3.4.3)
+
+**Merged pull requests:**
+
+- consensus group name for pan reference [\#190](https://github.com/sanger-pathogens/Roary/pull/190) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.4.2](https://github.com/sanger-pathogens/Roary/tree/v3.4.2) (2015-10-12)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.1...v3.4.2)
+
+**Merged pull requests:**
+
+- Gene presence and absence rtab [\#189](https://github.com/sanger-pathogens/Roary/pull/189) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.4.1](https://github.com/sanger-pathogens/Roary/tree/v3.4.1) (2015-10-08)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.0...v3.4.1)
+
+**Implemented enhancements:**
+
+- Need protein lengths in the final spreadsheet [\#116](https://github.com/sanger-pathogens/Roary/issues/116)
+
+**Fixed bugs:**
+
+- Bio-RetrieveAssemblies-1.0.1 fails to install [\#151](https://github.com/sanger-pathogens/Roary/issues/151)
+
+**Merged pull requests:**
+
+- \* Proposed fix for CPANTS error. [\#187](https://github.com/sanger-pathogens/Roary/pull/187) ([manwar](https://github.com/manwar))
+
+## [v3.4.0](https://github.com/sanger-pathogens/Roary/tree/v3.4.0) (2015-10-07)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.4...v3.4.0)
+
+**Merged pull requests:**
+
+- Extra columns in spreadsheet with gene lengths [\#186](https://github.com/sanger-pathogens/Roary/pull/186) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.3.4](https://github.com/sanger-pathogens/Roary/tree/v3.3.4) (2015-10-07)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.3...v3.3.4)
+
+**Closed issues:**
+
+- EXCEPTION: Bio::Root::Exception could not read ...faa.intermediate.extracted.fa [\#175](https://github.com/sanger-pathogens/Roary/issues/175)
+
+**Merged pull requests:**
+
+- increase dependancy RAM [\#185](https://github.com/sanger-pathogens/Roary/pull/185) ([andrewjpage](https://github.com/andrewjpage))
+- Use lsf for gene alignment [\#184](https://github.com/sanger-pathogens/Roary/pull/184) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.3.3](https://github.com/sanger-pathogens/Roary/tree/v3.3.3) (2015-09-29)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.2...v3.3.3)
+
+**Merged pull requests:**
+
+- dont align if sequences same length and nearly the same [\#183](https://github.com/sanger-pathogens/Roary/pull/183) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.3.2](https://github.com/sanger-pathogens/Roary/tree/v3.3.2) (2015-09-28)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.1...v3.3.2)
+
+**Implemented enhancements:**
+
+- Use of temporary folders and files [\#177](https://github.com/sanger-pathogens/Roary/issues/177)
+
+**Merged pull requests:**
+
+- Duplicate sequences in pan genome reference fasta [\#182](https://github.com/sanger-pathogens/Roary/pull/182) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.3.1](https://github.com/sanger-pathogens/Roary/tree/v3.3.1) (2015-09-25)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.0...v3.3.1)
+
+**Merged pull requests:**
+
+- Fix usage text [\#181](https://github.com/sanger-pathogens/Roary/pull/181) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.3.0](https://github.com/sanger-pathogens/Roary/tree/v3.3.0) (2015-09-24)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.9...v3.3.0)
+
+**Fixed bugs:**
+
+- Check at least 2 gff files have been passed in [\#171](https://github.com/sanger-pathogens/Roary/issues/171)
+- Pentuple memory for worst case sCenario [\#170](https://github.com/sanger-pathogens/Roary/issues/170)
+- 00\_requires\_external.t missing "mafft" ? [\#168](https://github.com/sanger-pathogens/Roary/issues/168)
+
+**Merged pull requests:**
+
+- Check dependancies [\#180](https://github.com/sanger-pathogens/Roary/pull/180) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.2.9](https://github.com/sanger-pathogens/Roary/tree/v3.2.9) (2015-09-23)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.8...v3.2.9)
+
+**Implemented enhancements:**
+
+- Add --outdir option to avoid blatting current directory [\#176](https://github.com/sanger-pathogens/Roary/issues/176)
+
+**Fixed bugs:**
+
+- CPAN install failure "unknown option mafft" [\#169](https://github.com/sanger-pathogens/Roary/issues/169)
+
+**Closed issues:**
+
+- Error "Cant open file: \_uninflated\_mcl\_groups" [\#179](https://github.com/sanger-pathogens/Roary/issues/179)
+
+**Merged pull requests:**
+
+- Add the option to specify an output directory [\#178](https://github.com/sanger-pathogens/Roary/pull/178) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.2.8](https://github.com/sanger-pathogens/Roary/tree/v3.2.8) (2015-09-23)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.7...v3.2.8)
+
+## [v3.2.7](https://github.com/sanger-pathogens/Roary/tree/v3.2.7) (2015-09-02)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.6...v3.2.7)
+
+**Merged pull requests:**
+
+- count paralogs correctly when looking for differences in datasets [\#174](https://github.com/sanger-pathogens/Roary/pull/174) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.2.6](https://github.com/sanger-pathogens/Roary/tree/v3.2.6) (2015-09-02)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.5...v3.2.6)
+
+**Merged pull requests:**
+
+- revert core tree generation [\#173](https://github.com/sanger-pathogens/Roary/pull/173) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.2.5](https://github.com/sanger-pathogens/Roary/tree/v3.2.5) (2015-08-17)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.4...v3.2.5)
+
+**Merged pull requests:**
+
+- Verbose stats [\#172](https://github.com/sanger-pathogens/Roary/pull/172) ([andrewjpage](https://github.com/andrewjpage))
+- dont set bioperl version [\#167](https://github.com/sanger-pathogens/Roary/pull/167) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.2.4](https://github.com/sanger-pathogens/Roary/tree/v3.2.4) (2015-07-23)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.3...v3.2.4)
+
+**Merged pull requests:**
+
+- update readme citation [\#165](https://github.com/sanger-pathogens/Roary/pull/165) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.2.3](https://github.com/sanger-pathogens/Roary/tree/v3.2.3) (2015-07-22)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.1...v3.2.3)
+
+**Merged pull requests:**
+
+- update citation message [\#164](https://github.com/sanger-pathogens/Roary/pull/164) ([andrewjpage](https://github.com/andrewjpage))
+- Pass mafft through to alignment [\#163](https://github.com/sanger-pathogens/Roary/pull/163) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.2.1](https://github.com/sanger-pathogens/Roary/tree/v3.2.1) (2015-07-21)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.0...v3.2.1)
+
+## [v3.2.0](https://github.com/sanger-pathogens/Roary/tree/v3.2.0) (2015-07-20)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.2...v3.2.0)
+
+**Merged pull requests:**
+
+- Use mafft [\#162](https://github.com/sanger-pathogens/Roary/pull/162) ([andrewjpage](https://github.com/andrewjpage))
+- output summary file [\#161](https://github.com/sanger-pathogens/Roary/pull/161) ([andrewjpage](https://github.com/andrewjpage))
+- Pass through dont delete flag [\#160](https://github.com/sanger-pathogens/Roary/pull/160) ([andrewjpage](https://github.com/andrewjpage))
+- Assembly statistics [\#159](https://github.com/sanger-pathogens/Roary/pull/159) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.1.2](https://github.com/sanger-pathogens/Roary/tree/v3.1.2) (2015-07-13)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/3.1.2...v3.1.2)
+
+## [3.1.2](https://github.com/sanger-pathogens/Roary/tree/3.1.2) (2015-07-13)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.1...3.1.2)
+
+**Fixed bugs:**
+
+- prank seg fault [\#157](https://github.com/sanger-pathogens/Roary/issues/157)
+
+**Merged pull requests:**
+
+- Core gene missing files [\#158](https://github.com/sanger-pathogens/Roary/pull/158) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.1.1](https://github.com/sanger-pathogens/Roary/tree/v3.1.1) (2015-06-26)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.0...v3.1.1)
+
+**Closed issues:**
+
+- sadaf [\#154](https://github.com/sanger-pathogens/Roary/issues/154)
+
+## [v3.1.0](https://github.com/sanger-pathogens/Roary/tree/v3.1.0) (2015-06-22)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.3...v3.1.0)
+
+**Merged pull requests:**
+
+- Accessory binary tree [\#155](https://github.com/sanger-pathogens/Roary/pull/155) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.0.3](https://github.com/sanger-pathogens/Roary/tree/v3.0.3) (2015-06-15)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.2...v3.0.3)
+
+**Fixed bugs:**
+
+- Annotation missing in set\_difference\_unique\_set\_one/two\_statistics.csv files [\#137](https://github.com/sanger-pathogens/Roary/issues/137)
+
+**Merged pull requests:**
+
+- when creating core gene alignment, lookup sample names to genes in sp… [\#153](https://github.com/sanger-pathogens/Roary/pull/153) ([andrewjpage](https://github.com/andrewjpage))
+- Only align core files [\#150](https://github.com/sanger-pathogens/Roary/pull/150) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.0.2](https://github.com/sanger-pathogens/Roary/tree/v3.0.2) (2015-06-12)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.1...v3.0.2)
+
+**Implemented enhancements:**
+
+- Print out the version number [\#119](https://github.com/sanger-pathogens/Roary/issues/119)
+
+**Merged pull requests:**
+
+- Mafft and exonerate dependancies [\#149](https://github.com/sanger-pathogens/Roary/pull/149) ([andrewjpage](https://github.com/andrewjpage))
+- Add a version parameter and add in marcos plots code [\#148](https://github.com/sanger-pathogens/Roary/pull/148) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v3.0.1](https://github.com/sanger-pathogens/Roary/tree/v3.0.1) (2015-06-12)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.0...v3.0.1)
+
+**Fixed bugs:**
+
+- Use of -e switch gives multifasta file with N's only [\#132](https://github.com/sanger-pathogens/Roary/issues/132)
+
+## [v3.0.0](https://github.com/sanger-pathogens/Roary/tree/v3.0.0) (2015-06-11)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.4...v3.0.0)
+
+**Merged pull requests:**
+
+- Use prank for core genome alignments [\#147](https://github.com/sanger-pathogens/Roary/pull/147) ([andrewjpage](https://github.com/andrewjpage))
+- Accessory graph [\#146](https://github.com/sanger-pathogens/Roary/pull/146) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.3.4](https://github.com/sanger-pathogens/Roary/tree/v2.3.4) (2015-06-10)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.3...v2.3.4)
+
+## [v2.3.3](https://github.com/sanger-pathogens/Roary/tree/v2.3.3) (2015-06-08)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.2...v2.3.3)
+
+**Merged pull requests:**
+
+- Simplify perl dependency installation [\#145](https://github.com/sanger-pathogens/Roary/pull/145) ([bewt85](https://github.com/bewt85))
+- Pan genome reference [\#144](https://github.com/sanger-pathogens/Roary/pull/144) ([andrewjpage](https://github.com/andrewjpage))
+- Fix input files with duplicate IDs [\#143](https://github.com/sanger-pathogens/Roary/pull/143) ([andrewjpage](https://github.com/andrewjpage))
+- Test against different versions of GNU Parallel [\#142](https://github.com/sanger-pathogens/Roary/pull/142) ([bewt85](https://github.com/bewt85))
+
+## [v2.3.2](https://github.com/sanger-pathogens/Roary/tree/v2.3.2) (2015-06-08)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.1...v2.3.2)
+
+**Fixed bugs:**
+
+- GFF files derived from Prokka genbank raise errors [\#130](https://github.com/sanger-pathogens/Roary/issues/130)
+- MSG: Got a sequence without letters. Could not guess alphabet [\#127](https://github.com/sanger-pathogens/Roary/issues/127)
+
+**Merged pull requests:**
+
+- TravisCI only wants the major and minor version of perl [\#141](https://github.com/sanger-pathogens/Roary/pull/141) ([bewt85](https://github.com/bewt85))
+- Add TravisCI support [\#140](https://github.com/sanger-pathogens/Roary/pull/140) ([bewt85](https://github.com/bewt85))
+- Use locus tag when ID is missing from GFF [\#139](https://github.com/sanger-pathogens/Roary/pull/139) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.3.1](https://github.com/sanger-pathogens/Roary/tree/v2.3.1) (2015-06-02)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.0...v2.3.1)
+
+**Merged pull requests:**
+
+- Extract IDs from GFF file using Bio::Perl [\#138](https://github.com/sanger-pathogens/Roary/pull/138) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.3.0](https://github.com/sanger-pathogens/Roary/tree/v2.3.0) (2015-06-01)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.6...v2.3.0)
+
+**Closed issues:**
+
+- "cpan" command reports Bio::Roary as version '\(undef\)' [\#134](https://github.com/sanger-pathogens/Roary/issues/134)
+
+## [v2.2.6](https://github.com/sanger-pathogens/Roary/tree/v2.2.6) (2015-06-01)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.4...v2.2.6)
+
+**Closed issues:**
+
+- No tagged release for 2.2.3 [\#133](https://github.com/sanger-pathogens/Roary/issues/133)
+- Syntax \(?\) errors on perl 5.10.1 [\#128](https://github.com/sanger-pathogens/Roary/issues/128)
+
+**Merged pull requests:**
+
+- include version numbers for cpan [\#136](https://github.com/sanger-pathogens/Roary/pull/136) ([andrewjpage](https://github.com/andrewjpage))
+- New version number for contributed fix for issue \#128 [\#135](https://github.com/sanger-pathogens/Roary/pull/135) ([andrewjpage](https://github.com/andrewjpage))
+- gnu parallel switch for ubuntu [\#131](https://github.com/sanger-pathogens/Roary/pull/131) ([andrewjpage](https://github.com/andrewjpage))
+- Backward compatible deferencing of hashes [\#129](https://github.com/sanger-pathogens/Roary/pull/129) ([mgalardini](https://github.com/mgalardini))
+
+## [v2.2.4](https://github.com/sanger-pathogens/Roary/tree/v2.2.4) (2015-05-29)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.3...v2.2.4)
+
+**Closed issues:**
+
+- ERROR: cannot remove directory for split\_groups [\#115](https://github.com/sanger-pathogens/Roary/issues/115)
+- cleanup outputfiles [\#114](https://github.com/sanger-pathogens/Roary/issues/114)
+
+**Merged pull requests:**
+
+- Cleanup files [\#126](https://github.com/sanger-pathogens/Roary/pull/126) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.2.3](https://github.com/sanger-pathogens/Roary/tree/v2.2.3) (2015-05-21)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.2...v2.2.3)
+
+**Closed issues:**
+
+- Change QC so that it doesnt shred reads [\#117](https://github.com/sanger-pathogens/Roary/issues/117)
+- QC doesnt work outside sanger [\#112](https://github.com/sanger-pathogens/Roary/issues/112)
+
+**Merged pull requests:**
+
+- Update Kraken QC [\#125](https://github.com/sanger-pathogens/Roary/pull/125) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.2.2](https://github.com/sanger-pathogens/Roary/tree/v2.2.2) (2015-05-21)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.0...v2.2.2)
+
+**Closed issues:**
+
+- Hard-coded Sanger paths in some scripts [\#124](https://github.com/sanger-pathogens/Roary/issues/124)
+- You're missing some Perl dependancies [\#123](https://github.com/sanger-pathogens/Roary/issues/123)
+- Add support for GFF files from NCBI [\#120](https://github.com/sanger-pathogens/Roary/issues/120)
+
+**Merged pull requests:**
+
+- Fix usage text [\#122](https://github.com/sanger-pathogens/Roary/pull/122) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.2.0](https://github.com/sanger-pathogens/Roary/tree/v2.2.0) (2015-05-14)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.2...v2.2.0)
+
+**Closed issues:**
+
+- Verbose output with -v [\#113](https://github.com/sanger-pathogens/Roary/issues/113)
+
+**Merged pull requests:**
+
+- Accept genbank files [\#121](https://github.com/sanger-pathogens/Roary/pull/121) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.1.2](https://github.com/sanger-pathogens/Roary/tree/v2.1.2) (2015-05-12)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.1...v2.1.2)
+
+**Merged pull requests:**
+
+- Verbose output [\#118](https://github.com/sanger-pathogens/Roary/pull/118) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.1.1](https://github.com/sanger-pathogens/Roary/tree/v2.1.1) (2015-04-29)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.9...v2.1.1)
+
+**Merged pull requests:**
+
+- pass core definition into number of conserved genes plot [\#111](https://github.com/sanger-pathogens/Roary/pull/111) ([andrewjpage](https://github.com/andrewjpage))
+- Vary core definition [\#110](https://github.com/sanger-pathogens/Roary/pull/110) ([andrewjpage](https://github.com/andrewjpage))
+- Use block quotes in readme [\#109](https://github.com/sanger-pathogens/Roary/pull/109) ([bewt85](https://github.com/bewt85))
+
+## [v2.0.9](https://github.com/sanger-pathogens/Roary/tree/v2.0.9) (2015-04-20)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.8...v2.0.9)
+
+**Merged pull requests:**
+
+- Allow for multiple processors to be used [\#108](https://github.com/sanger-pathogens/Roary/pull/108) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.0.8](https://github.com/sanger-pathogens/Roary/tree/v2.0.8) (2015-04-09)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.7...v2.0.8)
+
+**Merged pull requests:**
+
+- Speedup [\#107](https://github.com/sanger-pathogens/Roary/pull/107) ([andrewjpage](https://github.com/andrewjpage))
+- new version 2.0.7 [\#106](https://github.com/sanger-pathogens/Roary/pull/106) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.0.7](https://github.com/sanger-pathogens/Roary/tree/v2.0.7) (2015-03-28)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.5...v2.0.7)
+
+**Merged pull requests:**
+
+- old splits [\#105](https://github.com/sanger-pathogens/Roary/pull/105) ([andrewjpage](https://github.com/andrewjpage))
+- Speedup split [\#104](https://github.com/sanger-pathogens/Roary/pull/104) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.0.5](https://github.com/sanger-pathogens/Roary/tree/v2.0.5) (2015-03-26)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.4...v2.0.5)
+
+**Merged pull requests:**
+
+- Stop deep recursion [\#103](https://github.com/sanger-pathogens/Roary/pull/103) ([andrewjpage](https://github.com/andrewjpage))
+- check programs installed [\#102](https://github.com/sanger-pathogens/Roary/pull/102) ([andrewjpage](https://github.com/andrewjpage))
+
+## [2.0.4](https://github.com/sanger-pathogens/Roary/tree/2.0.4) (2015-03-23)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.3...2.0.4)
+
+**Merged pull requests:**
+
+- File slurp tiny [\#101](https://github.com/sanger-pathogens/Roary/pull/101) ([andrewjpage](https://github.com/andrewjpage))
+- version 2.0.3 [\#100](https://github.com/sanger-pathogens/Roary/pull/100) ([andrewjpage](https://github.com/andrewjpage))
+
+## [2.0.3](https://github.com/sanger-pathogens/Roary/tree/2.0.3) (2015-03-17)
+[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.0...2.0.3)
+
+**Merged pull requests:**
+
+- Remove LSF support [\#99](https://github.com/sanger-pathogens/Roary/pull/99) ([andrewjpage](https://github.com/andrewjpage))
+- Dont set LSF as the default runner [\#98](https://github.com/sanger-pathogens/Roary/pull/98) ([andrewjpage](https://github.com/andrewjpage))
+- Rename directories to Roary [\#97](https://github.com/sanger-pathogens/Roary/pull/97) ([andrewjpage](https://github.com/andrewjpage))
+
+## [v2.0.0](https://github.com/sanger-pathogens/Roary/tree/v2.0.0) (2015-03-16)
+**Merged pull requests:**
+
+- Ship binaries [\#96](https://github.com/sanger-pathogens/Roary/pull/96) ([andrewjpage](https://github.com/andrewjpage))
+- Pad merged multifastas when data is missing [\#95](https://github.com/sanger-pathogens/Roary/pull/95) ([carlacummins](https://github.com/carlacummins))
+- Subsample reads [\#94](https://github.com/sanger-pathogens/Roary/pull/94) ([andrewjpage](https://github.com/andrewjpage))
+- Merge Carlas CGN [\#93](https://github.com/sanger-pathogens/Roary/pull/93) ([andrewjpage](https://github.com/andrewjpage))
+- rename spreadsheet [\#92](https://github.com/sanger-pathogens/Roary/pull/92) ([andrewjpage](https://github.com/andrewjpage))
+- Refactor out fasta grep [\#91](https://github.com/sanger-pathogens/Roary/pull/91) ([andrewjpage](https://github.com/andrewjpage))
+- remove fasta\_grep [\#90](https://github.com/sanger-pathogens/Roary/pull/90) ([andrewjpage](https://github.com/andrewjpage))
+- Add gnu parallel support [\#89](https://github.com/sanger-pathogens/Roary/pull/89) ([andrewjpage](https://github.com/andrewjpage))
+- Updated create\_pan\_genome help text to include -qc option [\#88](https://github.com/sanger-pathogens/Roary/pull/88) ([carlacummins](https://github.com/carlacummins))
+- QC report option added [\#87](https://github.com/sanger-pathogens/Roary/pull/87) ([carlacummins](https://github.com/carlacummins))
+- increase blastp min memory to 3gb from 100 [\#86](https://github.com/sanger-pathogens/Roary/pull/86) ([andrewjpage](https://github.com/andrewjpage))
+- Remove fastatranslate dependancy [\#85](https://github.com/sanger-pathogens/Roary/pull/85) ([andrewjpage](https://github.com/andrewjpage))
+- Queue set to basement if number of samples \> 600 \(previously 800\) [\#84](https://github.com/sanger-pathogens/Roary/pull/84) ([carlacummins](https://github.com/carlacummins))
+- Bug fix [\#83](https://github.com/sanger-pathogens/Roary/pull/83) ([carlacummins](https://github.com/carlacummins))
+- Added verbose stats option [\#82](https://github.com/sanger-pathogens/Roary/pull/82) ([carlacummins](https://github.com/carlacummins))
+- Group limit changed to 50,000 [\#81](https://github.com/sanger-pathogens/Roary/pull/81) ([carlacummins](https://github.com/carlacummins))
+- Multifastas not created when group limit \(default 8000\) exceeded [\#80](https://github.com/sanger-pathogens/Roary/pull/80) ([carlacummins](https://github.com/carlacummins))
+- allow for translation table to be passed in [\#79](https://github.com/sanger-pathogens/Roary/pull/79) ([andrewjpage](https://github.com/andrewjpage))
+- increase memory [\#78](https://github.com/sanger-pathogens/Roary/pull/78) ([andrewjpage](https://github.com/andrewjpage))
+- Allow user specify sorting when reordering spreadsheet against a tree [\#77](https://github.com/sanger-pathogens/Roary/pull/77) ([andrewjpage](https://github.com/andrewjpage))
+- Bug fixing [\#76](https://github.com/sanger-pathogens/Roary/pull/76) ([carlacummins](https://github.com/carlacummins))
+- Added AUTHORS file [\#75](https://github.com/sanger-pathogens/Roary/pull/75) ([aslett1](https://github.com/aslett1))
+- if theres more than 1k samples use basement for default analysis [\#74](https://github.com/sanger-pathogens/Roary/pull/74) ([andrewjpage](https://github.com/andrewjpage))
+- use long queue for more than 200 samples [\#73](https://github.com/sanger-pathogens/Roary/pull/73) ([andrewjpage](https://github.com/andrewjpage))
+- core alignment gets run with lsf [\#72](https://github.com/sanger-pathogens/Roary/pull/72) ([andrewjpage](https://github.com/andrewjpage))
+- Job runner ids lsf [\#71](https://github.com/sanger-pathogens/Roary/pull/71) ([andrewjpage](https://github.com/andrewjpage))
+- Core alignment missing file [\#70](https://github.com/sanger-pathogens/Roary/pull/70) ([andrewjpage](https://github.com/andrewjpage))
+- Core alignment missing file [\#69](https://github.com/sanger-pathogens/Roary/pull/69) ([andrewjpage](https://github.com/andrewjpage))
+- update error reporting [\#68](https://github.com/sanger-pathogens/Roary/pull/68) ([andrewjpage](https://github.com/andrewjpage))
+- Create core alignment from spreadsheet and multifasta files [\#67](https://github.com/sanger-pathogens/Roary/pull/67) ([andrewjpage](https://github.com/andrewjpage))
+- make script executable [\#66](https://github.com/sanger-pathogens/Roary/pull/66) ([andrewjpage](https://github.com/andrewjpage))
+- script to merge multifasta files together [\#65](https://github.com/sanger-pathogens/Roary/pull/65) ([andrewjpage](https://github.com/andrewjpage))
+- rename output gene multfastas and pass all sequences through [\#64](https://github.com/sanger-pathogens/Roary/pull/64) ([andrewjpage](https://github.com/andrewjpage))
+- Align genes at protein level and back translate to nucleotides [\#63](https://github.com/sanger-pathogens/Roary/pull/63) ([andrewjpage](https://github.com/andrewjpage))
+- Depth first search for reordering spreadsheet [\#62](https://github.com/sanger-pathogens/Roary/pull/62) ([andrewjpage](https://github.com/andrewjpage))
+- make the iterative cdhit script useful for standalone use [\#61](https://github.com/sanger-pathogens/Roary/pull/61) ([andrewjpage](https://github.com/andrewjpage))
+- query\_pan\_genome\_update\_text [\#60](https://github.com/sanger-pathogens/Roary/pull/60) ([andrewjpage](https://github.com/andrewjpage))
+- fix failing tests [\#59](https://github.com/sanger-pathogens/Roary/pull/59) ([andrewjpage](https://github.com/andrewjpage))
+- Create plot for % blast identity [\#58](https://github.com/sanger-pathogens/Roary/pull/58) ([andrewjpage](https://github.com/andrewjpage))
+- add a flag to keep intermediate files [\#57](https://github.com/sanger-pathogens/Roary/pull/57) ([andrewjpage](https://github.com/andrewjpage))
+- set the known gene names to black and rest to colours [\#56](https://github.com/sanger-pathogens/Roary/pull/56) ([andrewjpage](https://github.com/andrewjpage))
+- print fragment blocks [\#55](https://github.com/sanger-pathogens/Roary/pull/55) ([andrewjpage](https://github.com/andrewjpage))
+- Fix ordering of accessory [\#54](https://github.com/sanger-pathogens/Roary/pull/54) ([andrewjpage](https://github.com/andrewjpage))
+- fix r plots [\#53](https://github.com/sanger-pathogens/Roary/pull/53) ([andrewjpage](https://github.com/andrewjpage))
+- Overlapping proteins [\#52](https://github.com/sanger-pathogens/Roary/pull/52) ([andrewjpage](https://github.com/andrewjpage))
+- Gene order [\#51](https://github.com/sanger-pathogens/Roary/pull/51) ([andrewjpage](https://github.com/andrewjpage))
+- pass job runner to iterative cdhit [\#50](https://github.com/sanger-pathogens/Roary/pull/50) ([andrewjpage](https://github.com/andrewjpage))
+- iterative cdhit in a job [\#49](https://github.com/sanger-pathogens/Roary/pull/49) ([andrewjpage](https://github.com/andrewjpage))
+- Fix tests [\#48](https://github.com/sanger-pathogens/Roary/pull/48) ([andrewjpage](https://github.com/andrewjpage))
+- Prefilter optimisation [\#47](https://github.com/sanger-pathogens/Roary/pull/47) ([andrewjpage](https://github.com/andrewjpage))
+- dont split groups [\#46](https://github.com/sanger-pathogens/Roary/pull/46) ([andrewjpage](https://github.com/andrewjpage))
+- rename create plots R script [\#45](https://github.com/sanger-pathogens/Roary/pull/45) ([andrewjpage](https://github.com/andrewjpage))
+- cdhit should output full description of sequence name [\#44](https://github.com/sanger-pathogens/Roary/pull/44) ([andrewjpage](https://github.com/andrewjpage))
+- Gene count plot [\#43](https://github.com/sanger-pathogens/Roary/pull/43) ([andrewjpage](https://github.com/andrewjpage))
+- align gene multifasta files using muscle [\#42](https://github.com/sanger-pathogens/Roary/pull/42) ([andrewjpage](https://github.com/andrewjpage))
+- Reorder spreadsheet [\#41](https://github.com/sanger-pathogens/Roary/pull/41) ([andrewjpage](https://github.com/andrewjpage))
+- Reorder spreadsheet [\#40](https://github.com/sanger-pathogens/Roary/pull/40) ([andrewjpage](https://github.com/andrewjpage))
+- Speedup post analysis [\#39](https://github.com/sanger-pathogens/Roary/pull/39) ([andrewjpage](https://github.com/andrewjpage))
+- Presence and absence of genes [\#38](https://github.com/sanger-pathogens/Roary/pull/38) ([andrewjpage](https://github.com/andrewjpage))
+- split big groups based on annotation [\#37](https://github.com/sanger-pathogens/Roary/pull/37) ([andrewjpage](https://github.com/andrewjpage))
+- make multifasta files easier to sort [\#36](https://github.com/sanger-pathogens/Roary/pull/36) ([andrewjpage](https://github.com/andrewjpage))
+- dont wait in lfs scheduler [\#35](https://github.com/sanger-pathogens/Roary/pull/35) ([andrewjpage](https://github.com/andrewjpage))
+- run post analysis as a job [\#34](https://github.com/sanger-pathogens/Roary/pull/34) ([andrewjpage](https://github.com/andrewjpage))
+- annotate the names of the groups files [\#33](https://github.com/sanger-pathogens/Roary/pull/33) ([andrewjpage](https://github.com/andrewjpage))
+- Output all sequences making up pan genome in multifasta files [\#32](https://github.com/sanger-pathogens/Roary/pull/32) ([andrewjpage](https://github.com/andrewjpage))
+- Run external applications through lsf [\#31](https://github.com/sanger-pathogens/Roary/pull/31) ([andrewjpage](https://github.com/andrewjpage))
+- remove done dependancy job [\#30](https://github.com/sanger-pathogens/Roary/pull/30) ([andrewjpage](https://github.com/andrewjpage))
+- blocking job [\#29](https://github.com/sanger-pathogens/Roary/pull/29) ([andrewjpage](https://github.com/andrewjpage))
+- Filter unknowns in LSF jobs [\#28](https://github.com/sanger-pathogens/Roary/pull/28) ([andrewjpage](https://github.com/andrewjpage))
+- Pass job runner through to extract gffs [\#27](https://github.com/sanger-pathogens/Roary/pull/27) ([andrewjpage](https://github.com/andrewjpage))
+- Change case of GFF commandline class [\#26](https://github.com/sanger-pathogens/Roary/pull/26) ([andrewjpage](https://github.com/andrewjpage))
+- use LSF to do the inital parsing of input files [\#25](https://github.com/sanger-pathogens/Roary/pull/25) ([andrewjpage](https://github.com/andrewjpage))
+- renamed LICENSE [\#24](https://github.com/sanger-pathogens/Roary/pull/24) ([CraigPorter](https://github.com/CraigPorter))
+- GPL [\#23](https://github.com/sanger-pathogens/Roary/pull/23) ([andrewjpage](https://github.com/andrewjpage))
+- lsf memory in mb [\#22](https://github.com/sanger-pathogens/Roary/pull/22) ([andrewjpage](https://github.com/andrewjpage))
+- low complexity filtering [\#21](https://github.com/sanger-pathogens/Roary/pull/21) ([andrewjpage](https://github.com/andrewjpage))
+- inflate clusters where the representative gene is not the first [\#20](https://github.com/sanger-pathogens/Roary/pull/20) ([andrewjpage](https://github.com/andrewjpage))
+- report more sequences from blastp [\#19](https://github.com/sanger-pathogens/Roary/pull/19) ([andrewjpage](https://github.com/andrewjpage))
+- update tests for different input processing [\#18](https://github.com/sanger-pathogens/Roary/pull/18) ([andrewjpage](https://github.com/andrewjpage))
+- speedup extracting proteins from gff [\#17](https://github.com/sanger-pathogens/Roary/pull/17) ([andrewjpage](https://github.com/andrewjpage))
+- sort spreadsheet by number of isolates [\#16](https://github.com/sanger-pathogens/Roary/pull/16) ([andrewjpage](https://github.com/andrewjpage))
+- create spreadsheets of differences between sets [\#15](https://github.com/sanger-pathogens/Roary/pull/15) ([andrewjpage](https://github.com/andrewjpage))
+- Output statistics on groups [\#14](https://github.com/sanger-pathogens/Roary/pull/14) ([andrewjpage](https://github.com/andrewjpage))
+- Find the difference between isolates [\#13](https://github.com/sanger-pathogens/Roary/pull/13) ([andrewjpage](https://github.com/andrewjpage))
+- check if group is null [\#12](https://github.com/sanger-pathogens/Roary/pull/12) ([andrewjpage](https://github.com/andrewjpage))
+- catch undef [\#11](https://github.com/sanger-pathogens/Roary/pull/11) ([andrewjpage](https://github.com/andrewjpage))
+- tests for create pan genome script [\#10](https://github.com/sanger-pathogens/Roary/pull/10) ([andrewjpage](https://github.com/andrewjpage))
+- label fasta sequences with annotation ID [\#9](https://github.com/sanger-pathogens/Roary/pull/9) ([andrewjpage](https://github.com/andrewjpage))
+- extract proteomes from gffs and transfer anntotation as part of script [\#8](https://github.com/sanger-pathogens/Roary/pull/8) ([andrewjpage](https://github.com/andrewjpage))
+- transfer annotation [\#7](https://github.com/sanger-pathogens/Roary/pull/7) ([andrewjpage](https://github.com/andrewjpage))
+- speedup searching fastas [\#6](https://github.com/sanger-pathogens/Roary/pull/6) ([andrewjpage](https://github.com/andrewjpage))
+- typo in memory estimation [\#5](https://github.com/sanger-pathogens/Roary/pull/5) ([andrewjpage](https://github.com/andrewjpage))
+- run mcl and inflate results [\#4](https://github.com/sanger-pathogens/Roary/pull/4) ([andrewjpage](https://github.com/andrewjpage))
+- vary memory usage according to input file size [\#3](https://github.com/sanger-pathogens/Roary/pull/3) ([andrewjpage](https://github.com/andrewjpage))
+- working on real data [\#2](https://github.com/sanger-pathogens/Roary/pull/2) ([andrewjpage](https://github.com/andrewjpage))
+- Initial functionality [\#1](https://github.com/sanger-pathogens/Roary/pull/1) ([andrewjpage](https://github.com/andrewjpage))
+
=====================================
README.md
=====================================
@@ -1,36 +1,70 @@
-# Roary the pan genome pipeline
-For instructions on how to use the software, the input format and output formats, please see [the Roary website](http://sanger-pathogens.github.io/Roary).
-
-[](https://travis-ci.org/sanger-pathogens/Roary)
-
+# Roary - The pan genome pipeline
+Takes annotated assemblies in GFF3 format and calculates the pan genome.
+
+PLEASE NOTE: we currently do not have the resources to provide support for Roary, so please do not expect a reply if you flag any issue.
+
+[](http://unmaintained.tech/)
+[](https://travis-ci.org/sanger-pathogens/Roary)
+[](https://github.com/sanger-pathogens/roary/blob/master/GPL-LICENSE)
+[](https://academic.oup.com/bioinformatics/article/31/22/3691/240757)
+[](http://bioconda.github.io/recipes/roary/README.html)
+[](https://quay.io/repository/biocontainers/roary)
+[](https://hub.docker.com/r/sangerpathogens/roary)
+[](https://hub.docker.com/r/sangerpathogens/roary)
+[](https://codecov.io/gh/sanger-pathogens/roary)
+
+## Contents
+ * [Introduction](#introduction)
+ * [Installation](#installation)
+ * [Required dependencies](#required-dependencies)
+ * [Optional dependencies](#optional-dependencies)
+ * [Ubuntu/Debian](#ubuntudebian)
+ * [Debian Testing](#debian-testing)
+ * [Ubuntu 14\.04/16\.04](#ubuntu-14041604)
+ * [Ubuntu 12\.04](#ubuntu-1204)
+ * [Bioconda \- OSX/Linux](#bioconda---osxlinux)
+ * [Galaxy](#galaxy)
+ * [GNU Guix](#gnu-guix)
+ * [Virtual Machine \- OSX/Linux/Windows](#virtual-machine---osxlinuxwindows)
+ * [Docker \- OSX/Linux/Windows/Cloud](#docker---osxlinuxwindowscloud)
+ * [Installing from source (advanced Linux users only)](#installing-from-source-advanced-linux-users-only)
+ * [Ancient systems and versions of perl](#ancient-systems-and-versions-of-perl)
+ * [Running the tests](#running-the-tests)
+ * [Versions of software we test against](#versions-of-software-we-test-against)
+ * [Usage](#usage)
+ * [License](#license)
+ * [Feedback/Issues](#feedbackissues)
+ * [Citation](#citation)
+ * [Further Information](#further-information)
+
+## Introduction
Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka) and calculates the pan genome. Using a standard desktop PC, it can analyse datasets with thousands of samples, something which is computationally infeasible with existing methods, without compromising the quality of the results. 128 samples can be analysed in under 1 hour using 1 GB of RAM and a single processor. To perform this analysis using existing methods would take weeks and hundreds of GB of RAM.
-## Citation
- "Roary: Rapid large-scale prokaryote pan genome analysis",
- Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
- Bioinformatics, (2015). doi: http://dx.doi.org/10.1093/bioinformatics/btv421
-[Roary: Rapid large-scale prokaryote pan genome analysis](http://dx.doi.org/10.1093/bioinformatics/btv421)
+## Installation
+Roary has the following dependencies:
+
+### Required dependencies
+* [bedtools](https://bedtools.readthedocs.io/en/latest/)
+* [cd-hit](http://weizhongli-lab.org/cd-hit/)
+* [ncbi-blast+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download)
+* [mcl](https://micans.org/mcl/)
+* [parallel](https://www.gnu.org/software/parallel/)
+* [prank](http://wasabiapp.org/software/prank/)
+* [mafft](https://mafft.cbrc.jp/alignment/software/)
+* [fasttree](http://www.microbesonline.org/fasttree/)
-# Installation
-Theres are a number of dependancies required for Roary, with instructions specific to the type of system you have:
-* Ubuntu/Debian
-* CentOS/RedHat
-* Bioconda - OSX/Linux
-* Galaxy
-* Guix - Linux
-* Virtual Machine - OSX/Linux/Windows
-* Docker - OSX/Linux/Windows/Cloud
-* Installing from source - OSX/Linux
+### Optional dependencies
+* [kraken](http://ccb.jhu.edu/software/kraken/MANUAL.html)
-If the installation fails please contact your system administrator. If you encounter a bug please let us know by emailing roary at sanger.ac.uk .
+There are a number of ways to install Roary and details are provided below. If you encounter an issue when installing Roary please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/Roary/issues) or email us at roary-help at sanger.ac.uk.
-## Ubuntu/Debian
-### Debian Testing
+### Ubuntu/Debian
+#### Debian Testing
```
sudo apt-get install roary
```
-### Ubuntu 14.04/16.04
+#### Ubuntu 14.04/16.04
All the dependancies can be installed using apt and cpanm. Root permissions are required. Ubuntu 16.04 contains a package for Roary but it is frozen at v3.6.0.
```
@@ -38,10 +72,10 @@ sudo apt-get install bedtools cd-hit ncbi-blast+ mcl parallel cpanminus prank ma
sudo cpanm -f Bio::Roary
```
-### Ubuntu 12.04
+#### Ubuntu 12.04
Some of the software versions in apt are quite old so follow the instructions for Bioconda below.
-## Bioconda - OSX/Linux
+### Bioconda - OSX/Linux
Install conda. Then install bioconda and roary:
```
@@ -52,23 +86,23 @@ conda config --add channels bioconda
conda install roary
```
-## Galaxy
-Roary is available from the Galaxy toolshed ( as is Prokka ).
+### Galaxy
+Roary is available from the Galaxy toolshed (as is Prokka).
-## GNU Guix
+### GNU Guix
Roary is included in [Guix](https://www.gnu.org/software/guix) and can be installed in the usual way:
```
guix package --install roary
```
-## Virtual Machine - OSX/Linux/Windows
+### Virtual Machine - OSX/Linux/Windows
Roary wont run natively on Windows but we have created virtual machine which has all of the software setup, including Prokka, 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 you're trying to do bioinformatics on Windows, you're not going to get very far and you should seriously consider upgrading to Linux.
-## Docker - OSX/Linux/Windows/Cloud
+### Docker - OSX/Linux/Windows/Cloud
We have a docker container which gets automatically built from the latest version of Roary in Debian Med. To install it:
```
@@ -80,7 +114,7 @@ To use it you would use a command such as this (substituting in your directories
docker run --rm -it -v /home/ubuntu/data:/data sangerpathogens/roary roary -f /data /data/*.gff
```
-## Installing from source (advanced Linux users only)
+### Installing from source (advanced Linux users only)
As a last resort you can install everything from source. This is for users with advanced Linux skills and we do not provide any support with this method since you have the skills to figure things out.
Download the latest software from (https://github.com/sanger-pathogens/Roary/tarball/master).
@@ -98,20 +132,27 @@ Add the following lines to your $HOME/.bashrc file, or to /etc/profile.d/roary.s
export PATH=$PATH:$HOME/Roary-x.x.x/bin
export PERL5LIB=$PERL5LIB:$HOME/Roary-x.x.x/lib
```
-Install the perl dependancies:
+Install the Perl dependencies:
```
-sudo cpanm Array::Utils Bio::Perl Exception::Class File::Basename File::Copy File::Find::Rule File::Grep File::Path File::Slurper File::Spec File::Temp File::Which FindBin Getopt::Long Graph Graph::Writer::Dot List::Util Log::Log4perl Moose Moose::Role Text::CSV PerlIO::utf8_strict
+sudo cpanm Array::Utils Bio::Perl Exception::Class File::Basename File::Copy File::Find::Rule File::Grep File::Path File::Slurper File::Spec File::Temp File::Which FindBin Getopt::Long Graph Graph::Writer::Dot List::Util Log::Log4perl Moose Moose::Role Text::CSV PerlIO::utf8_strict Devel::OverloadInfo Digest::MD5::File
```
Install the external dependances either from source or from your packaging system:
```
bedtools cd-hit blast mcl GNUparallel prank mafft fasttree
```
-## Ancient systems and versions of perl
+### Ancient systems and versions of perl
The code will not work with perl 5.8 or below (pre-modern perl). We no longer test against 5.10 (released 2007) or 5.12 (released 2010). If you're running a very old verison of Linux, you're also in trouble.
-# Versions of software we test against
+### Running the tests
+The test can be run with dzil from the top level directory:
+
+```
+dzil test
+```
+
+### Versions of software we test against
* Perl 5.14, 5.26
* cdhit 4.6.8
* ncbi blast+ 2.6.0
@@ -120,3 +161,59 @@ The code will not work with perl 5.8 or below (pre-modern perl). We no longer te
* prank 140603
* GNU parallel 20170822, 20160722
* FastTree 2.1.9
+
+## Usage
+```
+Usage: roary [options] *.gff
+
+Options: -p INT number of threads [1]
+ -o STR clusters output filename [clustered_proteins]
+ -f STR output directory [.]
+ -e create a multiFASTA alignment of core genes using PRANK
+ -n fast core gene alignment with MAFFT, use with -e
+ -i minimum percentage identity for blastp [95]
+ -cd FLOAT percentage of isolates a gene must be in to be core [99]
+ -qc generate QC report with Kraken
+ -k STR path to Kraken database for QC, use with -qc
+ -a check dependancies and print versions
+ -b STR blastp executable [blastp]
+ -c STR mcl executable [mcl]
+ -d STR mcxdeblast executable [mcxdeblast]
+ -g INT maximum number of clusters [50000]
+ -m STR makeblastdb executable [makeblastdb]
+ -r create R plots, requires R and ggplot2
+ -s dont split paralogs
+ -t INT translation table [11]
+ -ap allow paralogs in core alignment
+ -z dont delete intermediate files
+ -v verbose output to STDOUT
+ -w print version and exit
+ -y add gene inference information to spreadsheet, doesnt work with -e
+ -iv STR Change the MCL inflation value [1.5]
+ -h this help message
+
+Example: Quickly generate a core gene alignment using 8 threads
+ roary -e --mafft -p 8 *.gff
+
+For further info see: http://sanger-pathogens.github.io/Roary/
+```
+For further instructions on how to use the software, the input format and output formats, please see [the Roary website](http://sanger-pathogens.github.io/Roary).
+
+## License
+Roary is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/Roary/blob/master/GPL-LICENSE).
+
+## Feedback/Issues
+We currently do not have the resources to provide support for Roary. 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/Roary/issues).
+
+## Citation
+If you use this software please cite:
+
+ "Roary: Rapid large-scale prokaryote pan genome analysis",
+ Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,
+ Bioinformatics, (2015). doi: http://dx.doi.org/10.1093/bioinformatics/btv421
+[Roary: Rapid large-scale prokaryote pan genome analysis](http://dx.doi.org/10.1093/bioinformatics/btv421)
+
+## Further Information
+For more information on this software see:
+* [The Roary website](http://sanger-pathogens.github.io/Roary)
+* [The Jupyter notebook tutorial](https://github.com/sanger-pathogens/pathogen-informatics-training)
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+roary (3.13.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream release.
+ * Use debhelper 12.
+ * Bump Standards-Version.
+ * Update source lintian override location and tags.
+
+ -- Sascha Steinbiss <satta at debian.org> Fri, 08 Nov 2019 14:37:07 +0100
+
roary (3.12.0+dfsg-3) unstable; urgency=medium
* Fix support for BioPerl 1.7.4 package currently in unstable.
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-11
+12
=====================================
debian/control
=====================================
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Sascha Steinbiss <satta at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
dh-dist-zilla,
libdist-zilla-plugin-podweaver-perl,
bioperl (>= 1.7.4),
@@ -35,7 +35,7 @@ Build-Depends: debhelper (>= 11~),
mafft,
fasttree
Build-Depends-Indep: perl
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/roary
Vcs-Git: https://salsa.debian.org/med-team/roary.git
Homepage: http://sanger-pathogens.github.io/Roary/
=====================================
debian/source.lintian-overrides → debian/source/lintian-overrides
=====================================
@@ -1,2 +1,2 @@
# Upstream does not provide signed tarballs.
-roary source: debian-watch-may-check-gpg-signature
+roary source: debian-watch-does-not-check-gpg-signature
=====================================
dist.ini
=====================================
@@ -3,7 +3,7 @@ author = Andrew J. Page <ap13 at sanger.ac.uk>
license = GPL_3
copyright_holder = Wellcome Trust Sanger Institute
copyright_year = 2013
-version = 3.12.0
+version = 3.13.0
main_module = lib/Bio/Roary.pm
[MetaResources]
=====================================
lib/Bio/Roary/BedFromGFFRole.pm
=====================================
@@ -12,7 +12,7 @@ package Bio::Roary::BedFromGFFRole;
use Moose::Role;
use Bio::Tools::GFF;
-has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => '(CDS|ncRNA|tRNA|tmRNA|rRNA)' );
+has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => 'CDS' );
has 'min_gene_size_in_nucleotides' => ( is => 'ro', isa => 'Int', default => 18 );
has 'output_directory' => ( is => 'ro', isa => 'Str', default => '.' );
=====================================
lib/Bio/Roary/External/Cdhit.pm
=====================================
@@ -46,7 +46,7 @@ sub _build_memory_in_mb
$memory_required = -s $filename;
# Convert to mb
$memory_required = int($memory_required/1000000);
- # Triple memory for worst case senario
+ # Give it bucket loads of memory for the worst case scenario
$memory_required *= 5;
$memory_required = 2000 if($memory_required < 2000);
}
=====================================
lib/Bio/Roary/External/CheckTools.pm
=====================================
@@ -92,12 +92,12 @@ my %tools = (
my %cdhit_tools = (
'cdhit' => {
GETVER => "cdhit -h | grep 'CD-HIT version'",
- REGEXP => qr/version ($BIDEC) /,
+ REGEXP => qr/version\s+($BIDEC)/i,
MINVER => "4.6",
},
'cd-hit' => {
GETVER => "cd-hit -h | grep 'CD-HIT version'",
- REGEXP => qr/version ($BIDEC) /,
+ REGEXP => qr/version\s+($BIDEC)i/,
MINVER => "4.6",
}
);
=====================================
lib/Bio/Roary/ParseGFFAnnotationRole.pm
=====================================
@@ -12,7 +12,7 @@ use Bio::Tools::GFF;
has 'gff_file' => ( is => 'ro', isa => 'Str', required => 1 );
-has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => '(CDS|ncRNA|tRNA|tmRNA|rRNA)' );
+has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => 'CDS' );
has '_gff_parser' => ( is => 'ro', isa => 'Bio::Tools::GFF', lazy => 1, builder => '_build__gff_parser' );
has '_awk_filter' => ( is => 'ro', isa => 'Str', lazy => 1, builder => '_build__awk_filter' );
=====================================
lib/Bio/Roary/ReformatInputGFFs.pm
=====================================
@@ -27,7 +27,7 @@ use Digest::MD5::File qw(file_md5_hex);
has 'gff_files' => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'logger' => ( is => 'ro', lazy => 1, builder => '_build_logger' );
-has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => '(CDS|ncRNA|tRNA|tmRNA|rRNA)' );
+has '_tags_to_filter' => ( is => 'ro', isa => 'Str', default => 'CDS' );
has 'output_directory' => ( is => 'ro', isa => 'Str', default => 'fixed_input_files' );
has 'suffix_counter' => ( is => 'rw', isa => 'Int', default => 1 );
=====================================
t/Bio/Roary/ContigsToGeneIDsFromGFF.t
=====================================
@@ -23,7 +23,7 @@ is_deeply(
{
'abc|SC|contig000001' => [
'1_1', 'abc_00002', 'abc_00003', 'abc_00004', '1_2', 'abc_00006', '1_3', 'abc_00008',
- 'abc_01705', 'abc_00010', 'abc_00011', 'abc_00012', 'abc_00013', 'abc_00014', '1_6', 'abc_00016'
+ 'abc_00010', 'abc_00011', 'abc_00012', 'abc_00014', '1_6', 'abc_00016'
]
},
'Contigs match expected with standard output'
=====================================
t/data/example_annotation.gff.proteome.faa.expected
=====================================
@@ -41,16 +41,6 @@ FNNPSKPIGLFYNKEEAEQIQKEKGFIFVEDAGRGYRRVVPSPQPISIIELESIKTLIKN
DTLVIAAGGGGIPVIREQHDGFKGIDAVIDKDKTSALLGANIQCDQLIILTAIDYVYINF
NTENQQPLKTTNVDELKRYIDENQFAKGSMLPKIEAAISFIENNPKGSVLITSLNELDAA
LEGKVGTVIKK*
->abc_01705
-VENTINESEKKKRFKLKMPGAFMILFILTVVAVIATWVIPAGAYSKLSYEPSSQELKIVN
-PHNQVKKVPGTQQELDKMGVKIKIEQFKSGAINKPVSIPNTYERLKQHPAGPEQITSSMV
-EGTIEAVDIMVFILVLGGLIGVVQASGSFESGLLALTKKTKGHEFMLIVFVSILMIIGGT
-LCGIEEEAVAFYPILVPIFIALGYDSIVSVGAIFLASSVGSTFSTINPFSVVIASNAAGT
-TFTDGLYWRIGACIVGAIFVISYLYWYCKKIKNDPKASYSYEDKDAFEQQWSVLKDDDSA
-HFTLRKKIILTLFVLPFPIMVWGVMTQGWWFPVMASAFLIFTIIIMFIAGTGKSGLGEKG
-TVDAFVNGASSLVGVSLIIGLARGINLVLNEGMISDTILHFSSSLVQHMSGPLFIIVLLF
-IFFCLGFIVPSSSGLAVLSMPIFAPLADTVGIPRFVIVTTYQFGQYAMLFLAPTGLVMAT
-LQMLNMRYSHWFRFVWPVVAFVLIFGGGVLITQVLIYS*
>abc_00010
MTHLTKVLDTLTGICVVLLFSKYFVAYANMVFDWNLRWYLLENIPHLPIILFILMFIFGV
PSEMIKDRQRKNNGV*
=====================================
t/data/locus_tag_gffs/query_1.gff.proteome.faa.expected
=====================================
@@ -41,16 +41,6 @@ FNNPSKPIGLFYNKEEAEQIQKEKGFIFVEDAGRGYRRVVPSPQPISIIELESIKTLIKN
DTLVIAAGGGGIPVIREQHDGFKGIDAVIDKDKTSALLGANIQCDQLIILTAIDYVYINF
NTENQQPLKTTNVDELKRYIDENQFAKGSMLPKIEAAISFIENNPKGSVLITSLNELDAA
LEGKVGTVIKK*
->abc_01705
-VENTINESEKKKRFKLKMPGAFMILFILTVVAVIATWVIPAGAYSKLSYEPSSQELKIVN
-PHNQVKKVPGTQQELDKMGVKIKIEQFKSGAINKPVSIPNTYERLKQHPAGPEQITSSMV
-EGTIEAVDIMVFILVLGGLIGVVQASGSFESGLLALTKKTKGHEFMLIVFVSILMIIGGT
-LCGIEEEAVAFYPILVPIFIALGYDSIVSVGAIFLASSVGSTFSTINPFSVVIASNAAGT
-TFTDGLYWRIGACIVGAIFVISYLYWYCKKIKNDPKASYSYEDKDAFEQQWSVLKDDDSA
-HFTLRKKIILTLFVLPFPIMVWGVMTQGWWFPVMASAFLIFTIIIMFIAGTGKSGLGEKG
-TVDAFVNGASSLVGVSLIIGLARGINLVLNEGMISDTILHFSSSLVQHMSGPLFIIVLLF
-IFFCLGFIVPSSSGLAVLSMPIFAPLADTVGIPRFVIVTTYQFGQYAMLFLAPTGLVMAT
-LQMLNMRYSHWFRFVWPVVAFVLIFGGGVLITQVLIYS*
>abc_00010
MTHLTKVLDTLTGICVVLLFSKYFVAYANMVFDWNLRWYLLENIPHLPIILFILMFIFGV
PSEMIKDRQRKNNGV*
=====================================
t/data/locus_tag_gffs/query_2.gff.proteome.faa.expected
=====================================
@@ -41,16 +41,6 @@ FNNPSKPIGLFYNKEEAEQIQKEKGFIFVEDAGRGYRRVVPSPQPISIIELESIKTLIKN
DTLVIAAGGGGIPVIREQHDGFKGIDAVIDKDKTSALLGANIQCDQLIILTAIDYVYINF
NTENQQPLKTTNVDELKRYIDENQFAKGSMLPKIEAAISFIENNPKGSVLITSLNELDAA
LEGKVGTVIKK*
->zzz_01705
-VENTINESEKKKRFKLKMPGAFMILFILTVVAVIATWVIPAGAYSKLSYEPSSQELKIVN
-PHNQVKKVPGTQQELDKMGVKIKIEQFKSGAINKPVSIPNTYERLKQHPAGPEQITSSMV
-EGTIEAVDIMVFILVLGGLIGVVQASGSFESGLLALTKKTKGHEFMLIVFVSILMIIGGT
-LCGIEEEAVAFYPILVPIFIALGYDSIVSVGAIFLASSVGSTFSTINPFSVVIASNAAGT
-TFTDGLYWRIGACIVGAIFVISYLYWYCKKIKNDPKASYSYEDKDAFEQQWSVLKDDDSA
-HFTLRKKIILTLFVLPFPIMVWGVMTQGWWFPVMASAFLIFTIIIMFIAGTGKSGLGEKG
-TVDAFVNGASSLVGVSLIIGLARGINLVLNEGMISDTILHFSSSLVQHMSGPLFIIVLLF
-IFFCLGFIVPSSSGLAVLSMPIFAPLADTVGIPRFVIVTTYQFGQYAMLFLAPTGLVMAT
-LQMLNMRYSHWFRFVWPVVAFVLIFGGGVLITQVLIYS*
>zzz_00010
MTHLTKVLDTLTGICVVLLFSKYFVAYANMVFDWNLRWYLLENIPHLPIILFILMFIFGV
PSEMIKDRQRKNNGV*
=====================================
t/data/locus_tag_gffs/query_3.gff.proteome.faa.expected
=====================================
@@ -41,16 +41,6 @@ FNNPSKPIGLFYNKEEAEQIQKEKGFIFVEDAGRGYRRVVPSPQPISIIELESIKTLIKN
DTLVIAAGGGGIPVIREQHDGFKGIDAVIDKDKTSALLGANIQCDQLIILTAIDYVYINF
NTENQQPLKTTNVDELKRYIDENQFAKGSMLPKIEAAISFIENNPKGSVLITSLNELDAA
LEGKVGTVIKK*
->xxx_01705
-VENTINESEKKKRFKLKMPGAFMILFILTVVAVIATWVIPAGAYSKLSYEPSSQELKIVN
-PHNQVKKVPGTQQELDKMGVKIKIEQFKSGAINKPVSIPNTYERLKQHPAGPEQITSSMV
-EGTIEAVDIMVFILVLGGLIGVVQASGSFESGLLALTKKTKGHEFMLIVFVSILMIIGGT
-LCGIEEEAVAFYPILVPIFIALGYDSIVSVGAIFLASSVGSTFSTINPFSVVIASNAAGT
-TFTDGLYWRIGACIVGAIFVISYLYWYCKKIKNDPKASYSYEDKDAFEQQWSVLKDDDSA
-HFTLRKKIILTLFVLPFPIMVWGVMTQGWWFPVMASAFLIFTIIIMFIAGTGKSGLGEKG
-TVDAFVNGASSLVGVSLIIGLARGINLVLNEGMISDTILHFSSSLVQHMSGPLFIIVLLF
-IFFCLGFIVPSSSGLAVLSMPIFAPLADTVGIPRFVIVTTYQFGQYAMLFLAPTGLVMAT
-LQMLNMRYSHWFRFVWPVVAFVLIFGGGVLITQVLIYS*
>xxx_00010
MTHLTKVLDTLTGICVVLLFSKYFVAYANMVFDWNLRWYLLENIPHLPIILFILMFIFGV
PSEMIKDRQRKNNGV*
=====================================
t/data/overall_gene_presence_absence.csv
=====================================
@@ -13,7 +13,6 @@
"group_6","","superantigen-like protein","2","2","1","1","10","1","15","","725","725","725","abc_00006","05a85fcc1cbac7027ac3689992006154_6",""
"argF","","Ornithine carbamoyltransferase","2","2","1","1","9","1","14","","1001","1001","1001","1_3","05a85fcc1cbac7027ac3689992006154_7",""
"arcC1","","Carbamate kinase 1","2","2","1","1","8","1","13","","935","935","935","abc_00008","05a85fcc1cbac7027ac3689992006154_8",""
-"group_9","","16S ribosomal RNA","2","2","1","1","7","1","12","","1556","1556","1556","abc_01705","05a85fcc1cbac7027ac3689992006154_9",""
"group_16","","hypothetical protein","1","1","1","2","6","2","3","","146","146","146","","","abc_50002"
"group_17","argF","Ornithine carbamoyltransferase","1","1","1","2","5","2","4","","1001","1001","1001","","","3_3"
"group_18","","hypothetical protein","1","1","1","2","4","2","5","","227","227","227","","","abc_50010"
View it on GitLab: https://salsa.debian.org/med-team/roary/compare/ed24c0969829fd7776f4f8c702de98fc3a34f156...3703d0adc86a07d2983f4d65f8c5fcb40c0e006e
--
View it on GitLab: https://salsa.debian.org/med-team/roary/compare/ed24c0969829fd7776f4f8c702de98fc3a34f156...3703d0adc86a07d2983f4d65f8c5fcb40c0e006e
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