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CHANGELOG.md  view on Meta::CPAN

**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)