view release on metacpan or  search on metacpan

CHANGELOG.md  view on Meta::CPAN

- 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)

CHANGELOG.md  view on Meta::CPAN

**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))

CHANGELOG.md  view on Meta::CPAN

- 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)