Commit db170bf52d07e037f42547540ed7b528ca2338e2 - roary

Merge pull request #432 from ssjunnebo/add_changelog added changelog Sara Sjunnebo authored 5 years ago GitHub committed 5 years ago

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CHANGELOG.md less more

	0	# Change Log
	1
	2	## [Unreleased](https://github.com/sanger-pathogens/Roary/tree/HEAD)
	3
	4	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.12.0...HEAD)
	5
	6	Implemented enhancements:
	7
	8	- Feature Request: Clear error message for duplicated file names [\#363](https://github.com/sanger-pathogens/Roary/issues/363)
	9
	10	Fixed bugs:
	11
	12	- uninitialized value warning [\#297](https://github.com/sanger-pathogens/Roary/issues/297)
	13	- 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)
	14
	15	Closed issues:
	16
	17	- Interpretation accessory\_binary\_genes newick [\#429](https://github.com/sanger-pathogens/Roary/issues/429)
	18	- No gene annotation in gene\_presence\_absence.csv output [\#428](https://github.com/sanger-pathogens/Roary/issues/428)
	19	- Compilation aborted at pan\_genome\_post\_analysis [\#427](https://github.com/sanger-pathogens/Roary/issues/427)
	20	- Could not obtain pan\_genome\_sequences [\#426](https://github.com/sanger-pathogens/Roary/issues/426)
	21	- Pan genome for fungal genomes [\#425](https://github.com/sanger-pathogens/Roary/issues/425)
	22	- multifasta for all proteins [\#424](https://github.com/sanger-pathogens/Roary/issues/424)
	23	- roary\_plots.py KeyError: "X" not in index [\#423](https://github.com/sanger-pathogens/Roary/issues/423)
	24	- Confirm that use of BLAST's `-max\_target\_seqs` is intentional [\#422](https://github.com/sanger-pathogens/Roary/issues/422)
	25	- query\_pan\_genome 'Cant access file' error $Non-Working-Directory inputs$ [\#421](https://github.com/sanger-pathogens/Roary/issues/421)
	26	- How many .gff files does Roary need? [\#419](https://github.com/sanger-pathogens/Roary/issues/419)
	27	- Installation through Bioconda not working [\#418](https://github.com/sanger-pathogens/Roary/issues/418)
	28	- Is it possible to run roary without prokka output files? [\#417](https://github.com/sanger-pathogens/Roary/issues/417)
	29	- Exiting early because number of clusters is too high [\#415](https://github.com/sanger-pathogens/Roary/issues/415)
	30	- MSG: Got a sequence without letters. Could not guess alphabet? [\#414](https://github.com/sanger-pathogens/Roary/issues/414)
	31	- 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)
	32	- issues with running and empty files [\#411](https://github.com/sanger-pathogens/Roary/issues/411)
	33	- MSG: Got a sequence without letters. Could not guess alphabet [\#410](https://github.com/sanger-pathogens/Roary/issues/410)
	34	- moose.pm issue [\#407](https://github.com/sanger-pathogens/Roary/issues/407)
	35	- Tutorial data: extract\_proteome\_from\_gff [\#406](https://github.com/sanger-pathogens/Roary/issues/406)
	36	- Tutorial data: extract\_proteome\_from\_gff [\#403](https://github.com/sanger-pathogens/Roary/issues/403)
	37	- gene\_presence\_absence.csv incomplete [\#402](https://github.com/sanger-pathogens/Roary/issues/402)
	38	- Roary including non-protein coding features? [\#398](https://github.com/sanger-pathogens/Roary/issues/398)
	39	- Question: what programs can be used to visualize embl and dot files? [\#394](https://github.com/sanger-pathogens/Roary/issues/394)
	40	- Roary Does not terminated successfully [\#388](https://github.com/sanger-pathogens/Roary/issues/388)
	41	- python: can't open file 'roary\_plots.py': \[Errno 2\] No such file or directory [\#385](https://github.com/sanger-pathogens/Roary/issues/385)
	42	- Roary does not finish analysis even though cluster job queue returns successful completion [\#383](https://github.com/sanger-pathogens/Roary/issues/383)
	43	- Genes $well$ annotated in prokka end up all in different groups?? [\#355](https://github.com/sanger-pathogens/Roary/issues/355)
	44	- could not determine version of cd-hit [\#322](https://github.com/sanger-pathogens/Roary/issues/322)
	45	- Use of uninitialized value in require at $eval 792$ line 1. [\#308](https://github.com/sanger-pathogens/Roary/issues/308)
	46	- Error: unexpected input in "\_" [\#299](https://github.com/sanger-pathogens/Roary/issues/299)
	47	- inconsistent referencing of $TMPDIR ? [\#287](https://github.com/sanger-pathogens/Roary/issues/287)
	48
	49	Merged pull requests:
	50
	51	- Include tests in README [\#430](https://github.com/sanger-pathogens/Roary/pull/430) ([ssjunnebo](https://github.com/ssjunnebo))
	52	- 621556 badges [\#420](https://github.com/sanger-pathogens/Roary/pull/420) ([ssjunnebo](https://github.com/ssjunnebo))
	53	- Update roary\_plots from .ix to .loc [\#416](https://github.com/sanger-pathogens/Roary/pull/416) ([EvdH0](https://github.com/EvdH0))
	54	- Use only CDS features from GFF [\#400](https://github.com/sanger-pathogens/Roary/pull/400) ([embatty](https://github.com/embatty))
	55	- 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))
	56	- Avoid deprecation errors in roary\_plots [\#389](https://github.com/sanger-pathogens/Roary/pull/389) ([mgalardini](https://github.com/mgalardini))
	57
	58	## [v3.12.0](https://github.com/sanger-pathogens/Roary/tree/v3.12.0) (2018-01-23)
	59	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.4...v3.12.0)
	60
	61	Merged pull requests:
	62
	63	- Reduce min gene size [\#384](https://github.com/sanger-pathogens/Roary/pull/384) ([ssjunnebo](https://github.com/ssjunnebo))
	64
	65	## [v3.11.4](https://github.com/sanger-pathogens/Roary/tree/v3.11.4) (2018-01-16)
	66	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.3...v3.11.4)
	67
	68	Closed issues:
	69
	70	- Roary seemed to have stopped prematurely; any way to continue the run? [\#380](https://github.com/sanger-pathogens/Roary/issues/380)
	71	- Getting prank version without the online check [\#377](https://github.com/sanger-pathogens/Roary/issues/377)
	72	- Kraken version parsing error: [\#376](https://github.com/sanger-pathogens/Roary/issues/376)
	73	- 3.11.1 failing 2/55 $3/791$ tests [\#375](https://github.com/sanger-pathogens/Roary/issues/375)
	74	- Fix for prank version check [\#361](https://github.com/sanger-pathogens/Roary/issues/361)
	75	- mafft version check still failing - bug in regexp found [\#360](https://github.com/sanger-pathogens/Roary/issues/360)
	76	- roary -a =\> Use of uninitialized value in concatenation $.$ [\#270](https://github.com/sanger-pathogens/Roary/issues/270)
	77
	78	Merged pull requests:
	79
	80	- Fix dependancy checking option [\#382](https://github.com/sanger-pathogens/Roary/pull/382) ([andrewjpage](https://github.com/andrewjpage))
	81
	82	## [v3.11.3](https://github.com/sanger-pathogens/Roary/tree/v3.11.3) (2018-01-12)
	83	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.2...v3.11.3)
	84
	85	Merged pull requests:
	86
	87	- Version fix [\#379](https://github.com/sanger-pathogens/Roary/pull/379) ([andrewjpage](https://github.com/andrewjpage))
	88
	89	## [v3.11.2](https://github.com/sanger-pathogens/Roary/tree/v3.11.2) (2018-01-12)
	90	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.1...v3.11.2)
	91
	92	Fixed bugs:
	93
	94	- ExtractProteomeFromGff.t failing tests 3.11.0 [\#373](https://github.com/sanger-pathogens/Roary/issues/373)
	95
	96	Merged pull requests:
	97
	98	- fix mafft and kraken version extraction [\#378](https://github.com/sanger-pathogens/Roary/pull/378) ([andrewjpage](https://github.com/andrewjpage))
	99
	100	## [v3.11.1](https://github.com/sanger-pathogens/Roary/tree/v3.11.1) (2018-01-10)
	101	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.0...v3.11.1)
	102
	103	Closed issues:
	104
	105	- Sorting in version 3.11.0: uppercase letters first, lowercase second $non-alphabetical$ [\#371](https://github.com/sanger-pathogens/Roary/issues/371)
	106	- Genbank input [\#365](https://github.com/sanger-pathogens/Roary/issues/365)
	107	- not all annotated features are allocated to the clusters [\#359](https://github.com/sanger-pathogens/Roary/issues/359)
	108
	109	Merged pull requests:
	110
	111	- Bedtools getfasta format fix [\#374](https://github.com/sanger-pathogens/Roary/pull/374) ([andrewjpage](https://github.com/andrewjpage))
	112	- Update roary\_plots.py [\#372](https://github.com/sanger-pathogens/Roary/pull/372) ([franz89](https://github.com/franz89))
	113	- Issue \#363 add check for duplicate basenames [\#370](https://github.com/sanger-pathogens/Roary/pull/370) ([nickp60](https://github.com/nickp60))
	114	- README.md: Update Guix install instructions. [\#362](https://github.com/sanger-pathogens/Roary/pull/362) ([wwood](https://github.com/wwood))
	115
	116	## [v3.11.0](https://github.com/sanger-pathogens/Roary/tree/v3.11.0) (2017-10-10)
	117	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.2...v3.11.0)
	118
	119	Fixed bugs:
	120
	121	- Can't get version of kraken, kraken-report or mafft ? [\#312](https://github.com/sanger-pathogens/Roary/issues/312)
	122
	123	Closed issues:
	124
	125	- number\_of\_conserved\_genes.Rtab [\#354](https://github.com/sanger-pathogens/Roary/issues/354)
	126	- \[question\] Should it take this long? [\#352](https://github.com/sanger-pathogens/Roary/issues/352)
	127
	128	Merged pull requests:
	129
	130	- 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))
	131
	132	## [v3.10.2](https://github.com/sanger-pathogens/Roary/tree/v3.10.2) (2017-09-08)
	133	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.1...v3.10.2)
	134
	135	Closed issues:
	136
	137	- \[version 3.8.0\] Roary crashes at end on perl error message [\#323](https://github.com/sanger-pathogens/Roary/issues/323)
	138	- Cant open file: \_accessory\_clusters.clstr [\#320](https://github.com/sanger-pathogens/Roary/issues/320)
	139
	140	Merged pull requests:
	141
	142	- get kraken version [\#351](https://github.com/sanger-pathogens/Roary/pull/351) ([andrewjpage](https://github.com/andrewjpage))
	143
	144	## [v3.10.1](https://github.com/sanger-pathogens/Roary/tree/v3.10.1) (2017-09-07)
	145	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.0...v3.10.1)
	146
	147	Implemented enhancements:
	148
	149	- Auto-detect if input files are GFF or FASTA [\#348](https://github.com/sanger-pathogens/Roary/issues/348)
	150	- Can "Fixing input GFF files" be parallelized? [\#342](https://github.com/sanger-pathogens/Roary/issues/342)
	151
	152	Fixed bugs:
	153
	154	- The GNU General Public License, Version not specified [\#344](https://github.com/sanger-pathogens/Roary/issues/344)
	155
	156	Closed issues:
	157
	158	- MSG: The sequence does not appear to be FASTA format $lacks a descriptor line '\>'$ [\#346](https://github.com/sanger-pathogens/Roary/issues/346)
	159
	160	Merged pull requests:
	161
	162	- Improve input file handling [\#350](https://github.com/sanger-pathogens/Roary/pull/350) ([andrewjpage](https://github.com/andrewjpage))
	163
	164	## [v3.10.0](https://github.com/sanger-pathogens/Roary/tree/v3.10.0) (2017-09-07)
	165	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.1...v3.10.0)
	166
	167	Closed issues:
	168
	169	- Use of uninitialized value $Perl$ [\#345](https://github.com/sanger-pathogens/Roary/issues/345)
	170	- identical .gff file names from different genome, and then issue with mcl groups [\#341](https://github.com/sanger-pathogens/Roary/issues/341)
	171	- Cant open file: \_clustered.clstr [\#339](https://github.com/sanger-pathogens/Roary/issues/339)
	172
	173	## [v3.9.1](https://github.com/sanger-pathogens/Roary/tree/v3.9.1) (2017-08-22)
	174	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.0...v3.9.1)
	175
	176	Merged pull requests:
	177
	178	- Optionally allow paralogs in core gene alignment [\#343](https://github.com/sanger-pathogens/Roary/pull/343) ([andrewjpage](https://github.com/andrewjpage))
	179	- Script to find frequency of unique genes in samples [\#340](https://github.com/sanger-pathogens/Roary/pull/340) ([andrewjpage](https://github.com/andrewjpage))
	180
	181	## [v3.9.0](https://github.com/sanger-pathogens/Roary/tree/v3.9.0) (2017-08-09)
	182	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.2...v3.9.0)
	183
	184	Closed issues:
	185
	186	- roary\_plots: pangenome matrix tree does not look like input.newick tree [\#333](https://github.com/sanger-pathogens/Roary/issues/333)
	187	- use Roary with RAST files [\#332](https://github.com/sanger-pathogens/Roary/issues/332)
	188	- Roary [\#329](https://github.com/sanger-pathogens/Roary/issues/329)
	189	- sampling number is 10 in number of genes in pan and core genome [\#319](https://github.com/sanger-pathogens/Roary/issues/319)
	190
	191	Merged pull requests:
	192
	193	- Grammar edits [\#327](https://github.com/sanger-pathogens/Roary/pull/327) ([cgreene](https://github.com/cgreene))
	194	- allow for inflation factor for MCL to be changed [\#326](https://github.com/sanger-pathogens/Roary/pull/326) ([andrewjpage](https://github.com/andrewjpage))
	195
	196	## [v3.8.2](https://github.com/sanger-pathogens/Roary/tree/v3.8.2) (2017-05-21)
	197	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.1...v3.8.2)
	198
	199	## [v3.8.1](https://github.com/sanger-pathogens/Roary/tree/v3.8.1) (2017-05-21)
	200	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.0...v3.8.1)
	201
	202	Closed issues:
	203
	204	- BLAST Database error [\#321](https://github.com/sanger-pathogens/Roary/issues/321)
	205	- Results for same input differ always a bit $summary\_statistics.txt$ [\#318](https://github.com/sanger-pathogens/Roary/issues/318)
	206	- Error: Couldnt open GFF file [\#314](https://github.com/sanger-pathogens/Roary/issues/314)
	207	- Help with query\_pan\_genome [\#313](https://github.com/sanger-pathogens/Roary/issues/313)
	208
	209	Merged pull requests:
	210
	211	- update email address [\#325](https://github.com/sanger-pathogens/Roary/pull/325) ([ssjunnebo](https://github.com/ssjunnebo))
	212	- New option to roary\_plots.py [\#317](https://github.com/sanger-pathogens/Roary/pull/317) ([mgalardini](https://github.com/mgalardini))
	213
	214	## [v3.8.0](https://github.com/sanger-pathogens/Roary/tree/v3.8.0) (2017-01-25)
	215	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.1...v3.8.0)
	216
	217	Closed issues:
	218
	219	- Old version in the master tarball? [\#300](https://github.com/sanger-pathogens/Roary/issues/300)
	220	- prank is not installed $Linuxbrew$ [\#294](https://github.com/sanger-pathogens/Roary/issues/294)
	221	- roary\_plots.py problem [\#292](https://github.com/sanger-pathogens/Roary/issues/292)
	222
	223	Merged pull requests:
	224
	225	- Support latest version of blast [\#306](https://github.com/sanger-pathogens/Roary/pull/306) ([andrewjpage](https://github.com/andrewjpage))
	226	- infgen [\#305](https://github.com/sanger-pathogens/Roary/pull/305) ([andrewjpage](https://github.com/andrewjpage))
	227	- update from 108 to 118 [\#304](https://github.com/sanger-pathogens/Roary/pull/304) ([andrewjpage](https://github.com/andrewjpage))
	228	- update usage text for iterative CD-hit [\#301](https://github.com/sanger-pathogens/Roary/pull/301) ([andrewjpage](https://github.com/andrewjpage))
	229
	230	## [v3.7.1](https://github.com/sanger-pathogens/Roary/tree/v3.7.1) (2016-11-01)
	231	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.0...v3.7.1)
	232
	233	Closed issues:
	234
	235	- core\_gene\_alignment.aln missing [\#284](https://github.com/sanger-pathogens/Roary/issues/284)
	236	- Is these results fine to use? [\#282](https://github.com/sanger-pathogens/Roary/issues/282)
	237
	238	Merged pull requests:
	239
	240	- fix spelling [\#280](https://github.com/sanger-pathogens/Roary/pull/280) ([satta](https://github.com/satta))
	241	- dont add POD to end of R scripts [\#279](https://github.com/sanger-pathogens/Roary/pull/279) ([andrewjpage](https://github.com/andrewjpage))
	242
	243	## [v3.7.0](https://github.com/sanger-pathogens/Roary/tree/v3.7.0) (2016-09-23)
	244	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.9...v3.7.0)
	245
	246	## [v3.6.9](https://github.com/sanger-pathogens/Roary/tree/v3.6.9) (2016-09-22)
	247	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.8...v3.6.9)
	248
	249	Implemented enhancements:
	250
	251	- I have published a Roary homebrew formula [\#208](https://github.com/sanger-pathogens/Roary/issues/208)
	252	- Getting Roary into Homebrew [\#152](https://github.com/sanger-pathogens/Roary/issues/152)
	253
	254	Closed issues:
	255
	256	- roary\_plots.py missing [\#277](https://github.com/sanger-pathogens/Roary/issues/277)
	257	- Errors when downloaded sequences from NCBI [\#274](https://github.com/sanger-pathogens/Roary/issues/274)
	258	- Same dataset different results! [\#271](https://github.com/sanger-pathogens/Roary/issues/271)
	259	- \_clustered.clstr file does not exist, cannot be read [\#250](https://github.com/sanger-pathogens/Roary/issues/250)
	260
	261	Merged pull requests:
	262
	263	- Fixed easy-init warnings - 529655 [\#278](https://github.com/sanger-pathogens/Roary/pull/278) ([psweston](https://github.com/psweston))
	264	- README.md: Add instructions for GNU Guix. [\#273](https://github.com/sanger-pathogens/Roary/pull/273) ([wwood](https://github.com/wwood))
	265
	266	## [v3.6.8](https://github.com/sanger-pathogens/Roary/tree/v3.6.8) (2016-08-02)
	267	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.7...v3.6.8)
	268
	269	Merged pull requests:
	270
	271	- Allow gene names from gb [\#266](https://github.com/sanger-pathogens/Roary/pull/266) ([andrewjpage](https://github.com/andrewjpage))
	272	- Missing genes [\#265](https://github.com/sanger-pathogens/Roary/pull/265) ([andrewjpage](https://github.com/andrewjpage))
	273
	274	## [v3.6.7](https://github.com/sanger-pathogens/Roary/tree/v3.6.7) (2016-07-26)
	275	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.6...v3.6.7)
	276
	277	Fixed bugs:
	278
	279	- 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)
	280	- roary R plots don't work on server --- lack of X11 [\#194](https://github.com/sanger-pathogens/Roary/issues/194)
	281
	282	Closed issues:
	283
	284	- empty accessory\_binary\_genes.fa file [\#262](https://github.com/sanger-pathogens/Roary/issues/262)
	285	- a guix package [\#259](https://github.com/sanger-pathogens/Roary/issues/259)
	286	- create\_pan\_genome\_plots.R - X11 font problem [\#230](https://github.com/sanger-pathogens/Roary/issues/230)
	287	- Roary not generating pan\_genome\_reference.fa [\#223](https://github.com/sanger-pathogens/Roary/issues/223)
	288	- Roary not using packaged executables [\#215](https://github.com/sanger-pathogens/Roary/issues/215)
	289
	290	## [v3.6.6](https://github.com/sanger-pathogens/Roary/tree/v3.6.6) (2016-07-25)
	291	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.5...v3.6.6)
	292
	293	Fixed bugs:
	294
	295	- GFF parsing doesn't match GFF3 specification [\#249](https://github.com/sanger-pathogens/Roary/issues/249)
	296
	297	Merged pull requests:
	298
	299	- Fix empty accessory binary [\#264](https://github.com/sanger-pathogens/Roary/pull/264) ([andrewjpage](https://github.com/andrewjpage))
	300	- change to dist zilla starter bundle [\#261](https://github.com/sanger-pathogens/Roary/pull/261) ([nds](https://github.com/nds))
	301
	302	## [v3.6.5](https://github.com/sanger-pathogens/Roary/tree/v3.6.5) (2016-07-20)
	303	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.4...v3.6.5)
	304
	305	Merged pull requests:
	306
	307	- 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))
	308	- catch divide by zero error [\#258](https://github.com/sanger-pathogens/Roary/pull/258) ([andrewjpage](https://github.com/andrewjpage))
	309
	310	## [v3.6.4](https://github.com/sanger-pathogens/Roary/tree/v3.6.4) (2016-07-06)
	311	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.3...v3.6.4)
	312
	313	Merged pull requests:
	314
	315	- 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))
	316
	317	## [v3.6.3](https://github.com/sanger-pathogens/Roary/tree/v3.6.3) (2016-07-01)
	318	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.2...v3.6.3)
	319
	320	Merged pull requests:
	321
	322	- Speed up alignments [\#256](https://github.com/sanger-pathogens/Roary/pull/256) ([andrewjpage](https://github.com/andrewjpage))
	323
	324	## [v3.6.2](https://github.com/sanger-pathogens/Roary/tree/v3.6.2) (2016-05-10)
	325	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.1...v3.6.2)
	326
	327	Implemented enhancements:
	328
	329	- Prefix utility commands with roary- ? [\#226](https://github.com/sanger-pathogens/Roary/issues/226)
	330
	331	Merged pull requests:
	332
	333	- 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))
	334	- get rid of warning message [\#246](https://github.com/sanger-pathogens/Roary/pull/246) ([satta](https://github.com/satta))
	335
	336	## [v3.6.1](https://github.com/sanger-pathogens/Roary/tree/v3.6.1) (2016-04-18)
	337	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.0...v3.6.1)
	338
	339	Fixed bugs:
	340
	341	- roary\_plots.py generating flawed plots [\#221](https://github.com/sanger-pathogens/Roary/issues/221)
	342
	343	Closed issues:
	344
	345	- Core gene file missing error [\#241](https://github.com/sanger-pathogens/Roary/issues/241)
	346
	347	Merged pull requests:
	348
	349	- prefix commands with roary [\#244](https://github.com/sanger-pathogens/Roary/pull/244) ([andrewjpage](https://github.com/andrewjpage))
	350	- More improvements to roary\_plots [\#240](https://github.com/sanger-pathogens/Roary/pull/240) ([mgalardini](https://github.com/mgalardini))
	351
	352	## [v3.6.0](https://github.com/sanger-pathogens/Roary/tree/v3.6.0) (2016-02-23)
	353	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.9...v3.6.0)
	354
	355	Fixed bugs:
	356
	357	- MSG: Got a sequence without letters. Could not guess alphabet [\#229](https://github.com/sanger-pathogens/Roary/issues/229)
	358
	359	Closed issues:
	360
	361	- 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)
	362	- How to use multiple switches in commandline? [\#232](https://github.com/sanger-pathogens/Roary/issues/232)
	363
	364	Merged pull requests:
	365
	366	- Improvements to roary\_plots [\#236](https://github.com/sanger-pathogens/Roary/pull/236) ([mgalardini](https://github.com/mgalardini))
	367	- Rollback 3 5 8 [\#235](https://github.com/sanger-pathogens/Roary/pull/235) ([andrewjpage](https://github.com/andrewjpage))
	368
	369	## [v3.5.9](https://github.com/sanger-pathogens/Roary/tree/v3.5.9) (2016-02-17)
	370	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.8...v3.5.9)
	371
	372	Implemented enhancements:
	373
	374	- What clusters end up in gene accessory\_binary\_genes.fa ? [\#225](https://github.com/sanger-pathogens/Roary/issues/225)
	375
	376	Closed issues:
	377
	378	- roary.github.io just prints HELLO [\#233](https://github.com/sanger-pathogens/Roary/issues/233)
	379
	380	Merged pull requests:
	381
	382	- Fix minor typo [\#231](https://github.com/sanger-pathogens/Roary/pull/231) ([abremges](https://github.com/abremges))
	383
	384	## [v3.5.8](https://github.com/sanger-pathogens/Roary/tree/v3.5.8) (2016-01-20)
	385	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.7...v3.5.8)
	386
	387	Implemented enhancements:
	388
	389	- Getting Roary into Debian Med [\#219](https://github.com/sanger-pathogens/Roary/issues/219)
	390	- Add embl output file mapping location of each core gene in the core genome alignment [\#192](https://github.com/sanger-pathogens/Roary/issues/192)
	391
	392	Closed issues:
	393
	394	- Error message: Cannot find the mcxdeblast executable, please ensure its in your PATH [\#217](https://github.com/sanger-pathogens/Roary/issues/217)
	395
	396	Merged pull requests:
	397
	398	- Provide full accessory for building binary tree [\#227](https://github.com/sanger-pathogens/Roary/pull/227) ([andrewjpage](https://github.com/andrewjpage))
	399	- 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))
	400	- Debian nitpicks [\#220](https://github.com/sanger-pathogens/Roary/pull/220) ([satta](https://github.com/satta))
	401	- Core alignment header file [\#218](https://github.com/sanger-pathogens/Roary/pull/218) ([andrewjpage](https://github.com/andrewjpage))
	402
	403	## [v3.5.7](https://github.com/sanger-pathogens/Roary/tree/v3.5.7) (2015-12-17)
	404	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.6...v3.5.7)
	405
	406	Closed issues:
	407
	408	- Roary not checking tools needed to run [\#214](https://github.com/sanger-pathogens/Roary/issues/214)
	409
	410	Merged pull requests:
	411
	412	- Core gene count [\#213](https://github.com/sanger-pathogens/Roary/pull/213) ([andrewjpage](https://github.com/andrewjpage))
	413
	414	## [v3.5.6](https://github.com/sanger-pathogens/Roary/tree/v3.5.6) (2015-12-01)
	415	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.5...v3.5.6)
	416
	417	Implemented enhancements:
	418
	419	- Non-issue, FYI regarding my 'roary2svg.pl' script [\#195](https://github.com/sanger-pathogens/Roary/issues/195)
	420
	421	Merged pull requests:
	422
	423	- add roary2svg script [\#212](https://github.com/sanger-pathogens/Roary/pull/212) ([andrewjpage](https://github.com/andrewjpage))
	424
	425	## [v3.5.5](https://github.com/sanger-pathogens/Roary/tree/v3.5.5) (2015-11-26)
	426	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.4...v3.5.5)
	427
	428	Merged pull requests:
	429
	430	- CD-hit threads limit [\#211](https://github.com/sanger-pathogens/Roary/pull/211) ([andrewjpage](https://github.com/andrewjpage))
	431
	432	## [v3.5.4](https://github.com/sanger-pathogens/Roary/tree/v3.5.4) (2015-11-26)
	433	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.3...v3.5.4)
	434
	435	Fixed bugs:
	436
	437	- Use of uninitialized value in require at $eval ..$ line 1. [\#204](https://github.com/sanger-pathogens/Roary/issues/204)
	438	- \[bug\] Newick files in 3.5.1 have branch lengths of 0.0 [\#202](https://github.com/sanger-pathogens/Roary/issues/202)
	439
	440	Merged pull requests:
	441
	442	- Accessory binary fasta contains all C's fix [\#210](https://github.com/sanger-pathogens/Roary/pull/210) ([andrewjpage](https://github.com/andrewjpage))
	443
	444	## [v3.5.3](https://github.com/sanger-pathogens/Roary/tree/v3.5.3) (2015-11-26)
	445	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.2...v3.5.3)
	446
	447	Implemented enhancements:
	448
	449	- Enhancement: roary -a to continue on if other parameters as well [\#207](https://github.com/sanger-pathogens/Roary/issues/207)
	450	- Make summary\_statistics a TAB/TSV file? [\#193](https://github.com/sanger-pathogens/Roary/issues/193)
	451
	452	Fixed bugs:
	453
	454	- roary --version should return 0 not 255 exit code [\#206](https://github.com/sanger-pathogens/Roary/issues/206)
	455	- Is the roary -a check complete? [\#205](https://github.com/sanger-pathogens/Roary/issues/205)
	456
	457	## [v3.5.2](https://github.com/sanger-pathogens/Roary/tree/v3.5.2) (2015-11-25)
	458	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.1...v3.5.2)
	459
	460	Fixed bugs:
	461
	462	- Use of uninitialized value in File::Slurper and Encode.pm [\#196](https://github.com/sanger-pathogens/Roary/issues/196)
	463
	464	Merged pull requests:
	465
	466	- Improved dependancy checking [\#209](https://github.com/sanger-pathogens/Roary/pull/209) ([andrewjpage](https://github.com/andrewjpage))
	467	- Lsf update gene alignments [\#201](https://github.com/sanger-pathogens/Roary/pull/201) ([andrewjpage](https://github.com/andrewjpage))
	468
	469	## [v3.5.1](https://github.com/sanger-pathogens/Roary/tree/v3.5.1) (2015-11-12)
	470	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.0...v3.5.1)
	471
	472	Fixed bugs:
	473
	474	- Accessory genes newick file contains full path of infividual files [\#200](https://github.com/sanger-pathogens/Roary/issues/200)
	475	- 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))
	476
	477	## [v3.5.0](https://github.com/sanger-pathogens/Roary/tree/v3.5.0) (2015-11-12)
	478	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.3...v3.5.0)
	479
	480	Merged pull requests:
	481
	482	- remove path from accessory tree [\#198](https://github.com/sanger-pathogens/Roary/pull/198) ([andrewjpage](https://github.com/andrewjpage))
	483
	484	## [v3.4.3](https://github.com/sanger-pathogens/Roary/tree/v3.4.3) (2015-11-11)
	485	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.2...v3.4.3)
	486
	487	Merged pull requests:
	488
	489	- consensus group name for pan reference [\#190](https://github.com/sanger-pathogens/Roary/pull/190) ([andrewjpage](https://github.com/andrewjpage))
	490
	491	## [v3.4.2](https://github.com/sanger-pathogens/Roary/tree/v3.4.2) (2015-10-12)
	492	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.1...v3.4.2)
	493
	494	Merged pull requests:
	495
	496	- Gene presence and absence rtab [\#189](https://github.com/sanger-pathogens/Roary/pull/189) ([andrewjpage](https://github.com/andrewjpage))
	497
	498	## [v3.4.1](https://github.com/sanger-pathogens/Roary/tree/v3.4.1) (2015-10-08)
	499	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.0...v3.4.1)
	500
	501	Implemented enhancements:
	502
	503	- Need protein lengths in the final spreadsheet [\#116](https://github.com/sanger-pathogens/Roary/issues/116)
	504
	505	Fixed bugs:
	506
	507	- Bio-RetrieveAssemblies-1.0.1 fails to install [\#151](https://github.com/sanger-pathogens/Roary/issues/151)
	508
	509	Merged pull requests:
	510
	511	- \* Proposed fix for CPANTS error. [\#187](https://github.com/sanger-pathogens/Roary/pull/187) ([manwar](https://github.com/manwar))
	512
	513	## [v3.4.0](https://github.com/sanger-pathogens/Roary/tree/v3.4.0) (2015-10-07)
	514	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.4...v3.4.0)
	515
	516	Merged pull requests:
	517
	518	- Extra columns in spreadsheet with gene lengths [\#186](https://github.com/sanger-pathogens/Roary/pull/186) ([andrewjpage](https://github.com/andrewjpage))
	519
	520	## [v3.3.4](https://github.com/sanger-pathogens/Roary/tree/v3.3.4) (2015-10-07)
	521	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.3...v3.3.4)
	522
	523	Closed issues:
	524
	525	- EXCEPTION: Bio::Root::Exception could not read ...faa.intermediate.extracted.fa [\#175](https://github.com/sanger-pathogens/Roary/issues/175)
	526
	527	Merged pull requests:
	528
	529	- increase dependancy RAM [\#185](https://github.com/sanger-pathogens/Roary/pull/185) ([andrewjpage](https://github.com/andrewjpage))
	530	- Use lsf for gene alignment [\#184](https://github.com/sanger-pathogens/Roary/pull/184) ([andrewjpage](https://github.com/andrewjpage))
	531
	532	## [v3.3.3](https://github.com/sanger-pathogens/Roary/tree/v3.3.3) (2015-09-29)
	533	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.2...v3.3.3)
	534
	535	Merged pull requests:
	536
	537	- dont align if sequences same length and nearly the same [\#183](https://github.com/sanger-pathogens/Roary/pull/183) ([andrewjpage](https://github.com/andrewjpage))
	538
	539	## [v3.3.2](https://github.com/sanger-pathogens/Roary/tree/v3.3.2) (2015-09-28)
	540	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.1...v3.3.2)
	541
	542	Implemented enhancements:
	543
	544	- Use of temporary folders and files [\#177](https://github.com/sanger-pathogens/Roary/issues/177)
	545
	546	Merged pull requests:
	547
	548	- Duplicate sequences in pan genome reference fasta [\#182](https://github.com/sanger-pathogens/Roary/pull/182) ([andrewjpage](https://github.com/andrewjpage))
	549
	550	## [v3.3.1](https://github.com/sanger-pathogens/Roary/tree/v3.3.1) (2015-09-25)
	551	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.0...v3.3.1)
	552
	553	Merged pull requests:
	554
	555	- Fix usage text [\#181](https://github.com/sanger-pathogens/Roary/pull/181) ([andrewjpage](https://github.com/andrewjpage))
	556
	557	## [v3.3.0](https://github.com/sanger-pathogens/Roary/tree/v3.3.0) (2015-09-24)
	558	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.9...v3.3.0)
	559
	560	Fixed bugs:
	561
	562	- Check at least 2 gff files have been passed in [\#171](https://github.com/sanger-pathogens/Roary/issues/171)
	563	- Pentuple memory for worst case sCenario [\#170](https://github.com/sanger-pathogens/Roary/issues/170)
	564	- 00\_requires\_external.t missing "mafft" ? [\#168](https://github.com/sanger-pathogens/Roary/issues/168)
	565
	566	Merged pull requests:
	567
	568	- Check dependancies [\#180](https://github.com/sanger-pathogens/Roary/pull/180) ([andrewjpage](https://github.com/andrewjpage))
	569
	570	## [v3.2.9](https://github.com/sanger-pathogens/Roary/tree/v3.2.9) (2015-09-23)
	571	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.8...v3.2.9)
	572
	573	Implemented enhancements:
	574
	575	- Add --outdir option to avoid blatting current directory [\#176](https://github.com/sanger-pathogens/Roary/issues/176)
	576
	577	Fixed bugs:
	578
	579	- CPAN install failure "unknown option mafft" [\#169](https://github.com/sanger-pathogens/Roary/issues/169)
	580
	581	Closed issues:
	582
	583	- Error "Cant open file: \_uninflated\_mcl\_groups" [\#179](https://github.com/sanger-pathogens/Roary/issues/179)
	584
	585	Merged pull requests:
	586
	587	- Add the option to specify an output directory [\#178](https://github.com/sanger-pathogens/Roary/pull/178) ([andrewjpage](https://github.com/andrewjpage))
	588
	589	## [v3.2.8](https://github.com/sanger-pathogens/Roary/tree/v3.2.8) (2015-09-23)
	590	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.7...v3.2.8)
	591
	592	## [v3.2.7](https://github.com/sanger-pathogens/Roary/tree/v3.2.7) (2015-09-02)
	593	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.6...v3.2.7)
	594
	595	Merged pull requests:
	596
	597	- count paralogs correctly when looking for differences in datasets [\#174](https://github.com/sanger-pathogens/Roary/pull/174) ([andrewjpage](https://github.com/andrewjpage))
	598
	599	## [v3.2.6](https://github.com/sanger-pathogens/Roary/tree/v3.2.6) (2015-09-02)
	600	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.5...v3.2.6)
	601
	602	Merged pull requests:
	603
	604	- revert core tree generation [\#173](https://github.com/sanger-pathogens/Roary/pull/173) ([andrewjpage](https://github.com/andrewjpage))
	605
	606	## [v3.2.5](https://github.com/sanger-pathogens/Roary/tree/v3.2.5) (2015-08-17)
	607	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.4...v3.2.5)
	608
	609	Merged pull requests:
	610
	611	- Verbose stats [\#172](https://github.com/sanger-pathogens/Roary/pull/172) ([andrewjpage](https://github.com/andrewjpage))
	612	- dont set bioperl version [\#167](https://github.com/sanger-pathogens/Roary/pull/167) ([andrewjpage](https://github.com/andrewjpage))
	613
	614	## [v3.2.4](https://github.com/sanger-pathogens/Roary/tree/v3.2.4) (2015-07-23)
	615	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.3...v3.2.4)
	616
	617	Merged pull requests:
	618
	619	- update readme citation [\#165](https://github.com/sanger-pathogens/Roary/pull/165) ([andrewjpage](https://github.com/andrewjpage))
	620
	621	## [v3.2.3](https://github.com/sanger-pathogens/Roary/tree/v3.2.3) (2015-07-22)
	622	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.1...v3.2.3)
	623
	624	Merged pull requests:
	625
	626	- update citation message [\#164](https://github.com/sanger-pathogens/Roary/pull/164) ([andrewjpage](https://github.com/andrewjpage))
	627	- Pass mafft through to alignment [\#163](https://github.com/sanger-pathogens/Roary/pull/163) ([andrewjpage](https://github.com/andrewjpage))
	628
	629	## [v3.2.1](https://github.com/sanger-pathogens/Roary/tree/v3.2.1) (2015-07-21)
	630	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.0...v3.2.1)
	631
	632	## [v3.2.0](https://github.com/sanger-pathogens/Roary/tree/v3.2.0) (2015-07-20)
	633	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.2...v3.2.0)
	634
	635	Merged pull requests:
	636
	637	- Use mafft [\#162](https://github.com/sanger-pathogens/Roary/pull/162) ([andrewjpage](https://github.com/andrewjpage))
	638	- output summary file [\#161](https://github.com/sanger-pathogens/Roary/pull/161) ([andrewjpage](https://github.com/andrewjpage))
	639	- Pass through dont delete flag [\#160](https://github.com/sanger-pathogens/Roary/pull/160) ([andrewjpage](https://github.com/andrewjpage))
	640	- Assembly statistics [\#159](https://github.com/sanger-pathogens/Roary/pull/159) ([andrewjpage](https://github.com/andrewjpage))
	641
	642	## [v3.1.2](https://github.com/sanger-pathogens/Roary/tree/v3.1.2) (2015-07-13)
	643	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/3.1.2...v3.1.2)
	644
	645	## [3.1.2](https://github.com/sanger-pathogens/Roary/tree/3.1.2) (2015-07-13)
	646	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.1...3.1.2)
	647
	648	Fixed bugs:
	649
	650	- prank seg fault [\#157](https://github.com/sanger-pathogens/Roary/issues/157)
	651
	652	Merged pull requests:
	653
	654	- Core gene missing files [\#158](https://github.com/sanger-pathogens/Roary/pull/158) ([andrewjpage](https://github.com/andrewjpage))
	655
	656	## [v3.1.1](https://github.com/sanger-pathogens/Roary/tree/v3.1.1) (2015-06-26)
	657	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.0...v3.1.1)
	658
	659	Closed issues:
	660
	661	- sadaf [\#154](https://github.com/sanger-pathogens/Roary/issues/154)
	662
	663	## [v3.1.0](https://github.com/sanger-pathogens/Roary/tree/v3.1.0) (2015-06-22)
	664	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.3...v3.1.0)
	665
	666	Merged pull requests:
	667
	668	- Accessory binary tree [\#155](https://github.com/sanger-pathogens/Roary/pull/155) ([andrewjpage](https://github.com/andrewjpage))
	669
	670	## [v3.0.3](https://github.com/sanger-pathogens/Roary/tree/v3.0.3) (2015-06-15)
	671	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.2...v3.0.3)
	672
	673	Fixed bugs:
	674
	675	- Annotation missing in set\_difference\_unique\_set\_one/two\_statistics.csv files [\#137](https://github.com/sanger-pathogens/Roary/issues/137)
	676
	677	Merged pull requests:
	678
	679	- 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))
	680	- Only align core files [\#150](https://github.com/sanger-pathogens/Roary/pull/150) ([andrewjpage](https://github.com/andrewjpage))
	681
	682	## [v3.0.2](https://github.com/sanger-pathogens/Roary/tree/v3.0.2) (2015-06-12)
	683	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.1...v3.0.2)
	684
	685	Implemented enhancements:
	686
	687	- Print out the version number [\#119](https://github.com/sanger-pathogens/Roary/issues/119)
	688
	689	Merged pull requests:
	690
	691	- Mafft and exonerate dependancies [\#149](https://github.com/sanger-pathogens/Roary/pull/149) ([andrewjpage](https://github.com/andrewjpage))
	692	- Add a version parameter and add in marcos plots code [\#148](https://github.com/sanger-pathogens/Roary/pull/148) ([andrewjpage](https://github.com/andrewjpage))
	693
	694	## [v3.0.1](https://github.com/sanger-pathogens/Roary/tree/v3.0.1) (2015-06-12)
	695	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.0...v3.0.1)
	696
	697	Fixed bugs:
	698
	699	- Use of -e switch gives multifasta file with N's only [\#132](https://github.com/sanger-pathogens/Roary/issues/132)
	700
	701	## [v3.0.0](https://github.com/sanger-pathogens/Roary/tree/v3.0.0) (2015-06-11)
	702	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.4...v3.0.0)
	703
	704	Merged pull requests:
	705
	706	- Use prank for core genome alignments [\#147](https://github.com/sanger-pathogens/Roary/pull/147) ([andrewjpage](https://github.com/andrewjpage))
	707	- Accessory graph [\#146](https://github.com/sanger-pathogens/Roary/pull/146) ([andrewjpage](https://github.com/andrewjpage))
	708
	709	## [v2.3.4](https://github.com/sanger-pathogens/Roary/tree/v2.3.4) (2015-06-10)
	710	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.3...v2.3.4)
	711
	712	## [v2.3.3](https://github.com/sanger-pathogens/Roary/tree/v2.3.3) (2015-06-08)
	713	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.2...v2.3.3)
	714
	715	Merged pull requests:
	716
	717	- Simplify perl dependency installation [\#145](https://github.com/sanger-pathogens/Roary/pull/145) ([bewt85](https://github.com/bewt85))
	718	- Pan genome reference [\#144](https://github.com/sanger-pathogens/Roary/pull/144) ([andrewjpage](https://github.com/andrewjpage))
	719	- Fix input files with duplicate IDs [\#143](https://github.com/sanger-pathogens/Roary/pull/143) ([andrewjpage](https://github.com/andrewjpage))
	720	- Test against different versions of GNU Parallel [\#142](https://github.com/sanger-pathogens/Roary/pull/142) ([bewt85](https://github.com/bewt85))
	721
	722	## [v2.3.2](https://github.com/sanger-pathogens/Roary/tree/v2.3.2) (2015-06-08)
	723	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.1...v2.3.2)
	724
	725	Fixed bugs:
	726
	727	- GFF files derived from Prokka genbank raise errors [\#130](https://github.com/sanger-pathogens/Roary/issues/130)
	728	- MSG: Got a sequence without letters. Could not guess alphabet [\#127](https://github.com/sanger-pathogens/Roary/issues/127)
	729
	730	Merged pull requests:
	731
	732	- TravisCI only wants the major and minor version of perl [\#141](https://github.com/sanger-pathogens/Roary/pull/141) ([bewt85](https://github.com/bewt85))
	733	- Add TravisCI support [\#140](https://github.com/sanger-pathogens/Roary/pull/140) ([bewt85](https://github.com/bewt85))
	734	- Use locus tag when ID is missing from GFF [\#139](https://github.com/sanger-pathogens/Roary/pull/139) ([andrewjpage](https://github.com/andrewjpage))
	735
	736	## [v2.3.1](https://github.com/sanger-pathogens/Roary/tree/v2.3.1) (2015-06-02)
	737	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.0...v2.3.1)
	738
	739	Merged pull requests:
	740
	741	- Extract IDs from GFF file using Bio::Perl [\#138](https://github.com/sanger-pathogens/Roary/pull/138) ([andrewjpage](https://github.com/andrewjpage))
	742
	743	## [v2.3.0](https://github.com/sanger-pathogens/Roary/tree/v2.3.0) (2015-06-01)
	744	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.6...v2.3.0)
	745
	746	Closed issues:
	747
	748	- "cpan" command reports Bio::Roary as version '$undef$' [\#134](https://github.com/sanger-pathogens/Roary/issues/134)
	749
	750	## [v2.2.6](https://github.com/sanger-pathogens/Roary/tree/v2.2.6) (2015-06-01)
	751	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.4...v2.2.6)
	752
	753	Closed issues:
	754
	755	- No tagged release for 2.2.3 [\#133](https://github.com/sanger-pathogens/Roary/issues/133)
	756	- Syntax $?$ errors on perl 5.10.1 [\#128](https://github.com/sanger-pathogens/Roary/issues/128)
	757
	758	Merged pull requests:
	759
	760	- include version numbers for cpan [\#136](https://github.com/sanger-pathogens/Roary/pull/136) ([andrewjpage](https://github.com/andrewjpage))
	761	- New version number for contributed fix for issue \#128 [\#135](https://github.com/sanger-pathogens/Roary/pull/135) ([andrewjpage](https://github.com/andrewjpage))
	762	- gnu parallel switch for ubuntu [\#131](https://github.com/sanger-pathogens/Roary/pull/131) ([andrewjpage](https://github.com/andrewjpage))
	763	- Backward compatible deferencing of hashes [\#129](https://github.com/sanger-pathogens/Roary/pull/129) ([mgalardini](https://github.com/mgalardini))
	764
	765	## [v2.2.4](https://github.com/sanger-pathogens/Roary/tree/v2.2.4) (2015-05-29)
	766	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.3...v2.2.4)
	767
	768	Closed issues:
	769
	770	- ERROR: cannot remove directory for split\_groups [\#115](https://github.com/sanger-pathogens/Roary/issues/115)
	771	- cleanup outputfiles [\#114](https://github.com/sanger-pathogens/Roary/issues/114)
	772
	773	Merged pull requests:
	774
	775	- Cleanup files [\#126](https://github.com/sanger-pathogens/Roary/pull/126) ([andrewjpage](https://github.com/andrewjpage))
	776
	777	## [v2.2.3](https://github.com/sanger-pathogens/Roary/tree/v2.2.3) (2015-05-21)
	778	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.2...v2.2.3)
	779
	780	Closed issues:
	781
	782	- Change QC so that it doesnt shred reads [\#117](https://github.com/sanger-pathogens/Roary/issues/117)
	783	- QC doesnt work outside sanger [\#112](https://github.com/sanger-pathogens/Roary/issues/112)
	784
	785	Merged pull requests:
	786
	787	- Update Kraken QC [\#125](https://github.com/sanger-pathogens/Roary/pull/125) ([andrewjpage](https://github.com/andrewjpage))
	788
	789	## [v2.2.2](https://github.com/sanger-pathogens/Roary/tree/v2.2.2) (2015-05-21)
	790	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.0...v2.2.2)
	791
	792	Closed issues:
	793
	794	- Hard-coded Sanger paths in some scripts [\#124](https://github.com/sanger-pathogens/Roary/issues/124)
	795	- You're missing some Perl dependancies [\#123](https://github.com/sanger-pathogens/Roary/issues/123)
	796	- Add support for GFF files from NCBI [\#120](https://github.com/sanger-pathogens/Roary/issues/120)
	797
	798	Merged pull requests:
	799
	800	- Fix usage text [\#122](https://github.com/sanger-pathogens/Roary/pull/122) ([andrewjpage](https://github.com/andrewjpage))
	801
	802	## [v2.2.0](https://github.com/sanger-pathogens/Roary/tree/v2.2.0) (2015-05-14)
	803	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.2...v2.2.0)
	804
	805	Closed issues:
	806
	807	- Verbose output with -v [\#113](https://github.com/sanger-pathogens/Roary/issues/113)
	808
	809	Merged pull requests:
	810
	811	- Accept genbank files [\#121](https://github.com/sanger-pathogens/Roary/pull/121) ([andrewjpage](https://github.com/andrewjpage))
	812
	813	## [v2.1.2](https://github.com/sanger-pathogens/Roary/tree/v2.1.2) (2015-05-12)
	814	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.1...v2.1.2)
	815
	816	Merged pull requests:
	817
	818	- Verbose output [\#118](https://github.com/sanger-pathogens/Roary/pull/118) ([andrewjpage](https://github.com/andrewjpage))
	819
	820	## [v2.1.1](https://github.com/sanger-pathogens/Roary/tree/v2.1.1) (2015-04-29)
	821	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.9...v2.1.1)
	822
	823	Merged pull requests:
	824
	825	- pass core definition into number of conserved genes plot [\#111](https://github.com/sanger-pathogens/Roary/pull/111) ([andrewjpage](https://github.com/andrewjpage))
	826	- Vary core definition [\#110](https://github.com/sanger-pathogens/Roary/pull/110) ([andrewjpage](https://github.com/andrewjpage))
	827	- Use block quotes in readme [\#109](https://github.com/sanger-pathogens/Roary/pull/109) ([bewt85](https://github.com/bewt85))
	828
	829	## [v2.0.9](https://github.com/sanger-pathogens/Roary/tree/v2.0.9) (2015-04-20)
	830	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.8...v2.0.9)
	831
	832	Merged pull requests:
	833
	834	- Allow for multiple processors to be used [\#108](https://github.com/sanger-pathogens/Roary/pull/108) ([andrewjpage](https://github.com/andrewjpage))
	835
	836	## [v2.0.8](https://github.com/sanger-pathogens/Roary/tree/v2.0.8) (2015-04-09)
	837	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.7...v2.0.8)
	838
	839	Merged pull requests:
	840
	841	- Speedup [\#107](https://github.com/sanger-pathogens/Roary/pull/107) ([andrewjpage](https://github.com/andrewjpage))
	842	- new version 2.0.7 [\#106](https://github.com/sanger-pathogens/Roary/pull/106) ([andrewjpage](https://github.com/andrewjpage))
	843
	844	## [v2.0.7](https://github.com/sanger-pathogens/Roary/tree/v2.0.7) (2015-03-28)
	845	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.5...v2.0.7)
	846
	847	Merged pull requests:
	848
	849	- old splits [\#105](https://github.com/sanger-pathogens/Roary/pull/105) ([andrewjpage](https://github.com/andrewjpage))
	850	- Speedup split [\#104](https://github.com/sanger-pathogens/Roary/pull/104) ([andrewjpage](https://github.com/andrewjpage))
	851
	852	## [v2.0.5](https://github.com/sanger-pathogens/Roary/tree/v2.0.5) (2015-03-26)
	853	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.4...v2.0.5)
	854
	855	Merged pull requests:
	856
	857	- Stop deep recursion [\#103](https://github.com/sanger-pathogens/Roary/pull/103) ([andrewjpage](https://github.com/andrewjpage))
	858	- check programs installed [\#102](https://github.com/sanger-pathogens/Roary/pull/102) ([andrewjpage](https://github.com/andrewjpage))
	859
	860	## [2.0.4](https://github.com/sanger-pathogens/Roary/tree/2.0.4) (2015-03-23)
	861	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.3...2.0.4)
	862
	863	Merged pull requests:
	864
	865	- File slurp tiny [\#101](https://github.com/sanger-pathogens/Roary/pull/101) ([andrewjpage](https://github.com/andrewjpage))
	866	- version 2.0.3 [\#100](https://github.com/sanger-pathogens/Roary/pull/100) ([andrewjpage](https://github.com/andrewjpage))
	867
	868	## [2.0.3](https://github.com/sanger-pathogens/Roary/tree/2.0.3) (2015-03-17)
	869	[Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.0...2.0.3)
	870
	871	Merged pull requests:
	872
	873	- Remove LSF support [\#99](https://github.com/sanger-pathogens/Roary/pull/99) ([andrewjpage](https://github.com/andrewjpage))
	874	- Dont set LSF as the default runner [\#98](https://github.com/sanger-pathogens/Roary/pull/98) ([andrewjpage](https://github.com/andrewjpage))
	875	- Rename directories to Roary [\#97](https://github.com/sanger-pathogens/Roary/pull/97) ([andrewjpage](https://github.com/andrewjpage))
	876
	877	## [v2.0.0](https://github.com/sanger-pathogens/Roary/tree/v2.0.0) (2015-03-16)
	878	Merged pull requests:
	879
	880	- Ship binaries [\#96](https://github.com/sanger-pathogens/Roary/pull/96) ([andrewjpage](https://github.com/andrewjpage))
	881	- Pad merged multifastas when data is missing [\#95](https://github.com/sanger-pathogens/Roary/pull/95) ([carlacummins](https://github.com/carlacummins))
	882	- Subsample reads [\#94](https://github.com/sanger-pathogens/Roary/pull/94) ([andrewjpage](https://github.com/andrewjpage))
	883	- Merge Carlas CGN [\#93](https://github.com/sanger-pathogens/Roary/pull/93) ([andrewjpage](https://github.com/andrewjpage))
	884	- rename spreadsheet [\#92](https://github.com/sanger-pathogens/Roary/pull/92) ([andrewjpage](https://github.com/andrewjpage))
	885	- Refactor out fasta grep [\#91](https://github.com/sanger-pathogens/Roary/pull/91) ([andrewjpage](https://github.com/andrewjpage))
	886	- remove fasta\_grep [\#90](https://github.com/sanger-pathogens/Roary/pull/90) ([andrewjpage](https://github.com/andrewjpage))
	887	- Add gnu parallel support [\#89](https://github.com/sanger-pathogens/Roary/pull/89) ([andrewjpage](https://github.com/andrewjpage))
	888	- Updated create\_pan\_genome help text to include -qc option [\#88](https://github.com/sanger-pathogens/Roary/pull/88) ([carlacummins](https://github.com/carlacummins))
	889	- QC report option added [\#87](https://github.com/sanger-pathogens/Roary/pull/87) ([carlacummins](https://github.com/carlacummins))
	890	- increase blastp min memory to 3gb from 100 [\#86](https://github.com/sanger-pathogens/Roary/pull/86) ([andrewjpage](https://github.com/andrewjpage))
	891	- Remove fastatranslate dependancy [\#85](https://github.com/sanger-pathogens/Roary/pull/85) ([andrewjpage](https://github.com/andrewjpage))
	892	- 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))
	893	- Bug fix [\#83](https://github.com/sanger-pathogens/Roary/pull/83) ([carlacummins](https://github.com/carlacummins))
	894	- Added verbose stats option [\#82](https://github.com/sanger-pathogens/Roary/pull/82) ([carlacummins](https://github.com/carlacummins))
	895	- Group limit changed to 50,000 [\#81](https://github.com/sanger-pathogens/Roary/pull/81) ([carlacummins](https://github.com/carlacummins))
	896	- Multifastas not created when group limit $default 8000$ exceeded [\#80](https://github.com/sanger-pathogens/Roary/pull/80) ([carlacummins](https://github.com/carlacummins))
	897	- allow for translation table to be passed in [\#79](https://github.com/sanger-pathogens/Roary/pull/79) ([andrewjpage](https://github.com/andrewjpage))
	898	- increase memory [\#78](https://github.com/sanger-pathogens/Roary/pull/78) ([andrewjpage](https://github.com/andrewjpage))
	899	- Allow user specify sorting when reordering spreadsheet against a tree [\#77](https://github.com/sanger-pathogens/Roary/pull/77) ([andrewjpage](https://github.com/andrewjpage))
	900	- Bug fixing [\#76](https://github.com/sanger-pathogens/Roary/pull/76) ([carlacummins](https://github.com/carlacummins))
	901	- Added AUTHORS file [\#75](https://github.com/sanger-pathogens/Roary/pull/75) ([aslett1](https://github.com/aslett1))
	902	- 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))
	903	- use long queue for more than 200 samples [\#73](https://github.com/sanger-pathogens/Roary/pull/73) ([andrewjpage](https://github.com/andrewjpage))
	904	- core alignment gets run with lsf [\#72](https://github.com/sanger-pathogens/Roary/pull/72) ([andrewjpage](https://github.com/andrewjpage))
	905	- Job runner ids lsf [\#71](https://github.com/sanger-pathogens/Roary/pull/71) ([andrewjpage](https://github.com/andrewjpage))
	906	- Core alignment missing file [\#70](https://github.com/sanger-pathogens/Roary/pull/70) ([andrewjpage](https://github.com/andrewjpage))
	907	- Core alignment missing file [\#69](https://github.com/sanger-pathogens/Roary/pull/69) ([andrewjpage](https://github.com/andrewjpage))
	908	- update error reporting [\#68](https://github.com/sanger-pathogens/Roary/pull/68) ([andrewjpage](https://github.com/andrewjpage))
	909	- Create core alignment from spreadsheet and multifasta files [\#67](https://github.com/sanger-pathogens/Roary/pull/67) ([andrewjpage](https://github.com/andrewjpage))
	910	- make script executable [\#66](https://github.com/sanger-pathogens/Roary/pull/66) ([andrewjpage](https://github.com/andrewjpage))
	911	- script to merge multifasta files together [\#65](https://github.com/sanger-pathogens/Roary/pull/65) ([andrewjpage](https://github.com/andrewjpage))
	912	- rename output gene multfastas and pass all sequences through [\#64](https://github.com/sanger-pathogens/Roary/pull/64) ([andrewjpage](https://github.com/andrewjpage))
	913	- Align genes at protein level and back translate to nucleotides [\#63](https://github.com/sanger-pathogens/Roary/pull/63) ([andrewjpage](https://github.com/andrewjpage))
	914	- Depth first search for reordering spreadsheet [\#62](https://github.com/sanger-pathogens/Roary/pull/62) ([andrewjpage](https://github.com/andrewjpage))
	915	- make the iterative cdhit script useful for standalone use [\#61](https://github.com/sanger-pathogens/Roary/pull/61) ([andrewjpage](https://github.com/andrewjpage))
	916	- query\_pan\_genome\_update\_text [\#60](https://github.com/sanger-pathogens/Roary/pull/60) ([andrewjpage](https://github.com/andrewjpage))
	917	- fix failing tests [\#59](https://github.com/sanger-pathogens/Roary/pull/59) ([andrewjpage](https://github.com/andrewjpage))
	918	- Create plot for % blast identity [\#58](https://github.com/sanger-pathogens/Roary/pull/58) ([andrewjpage](https://github.com/andrewjpage))
	919	- add a flag to keep intermediate files [\#57](https://github.com/sanger-pathogens/Roary/pull/57) ([andrewjpage](https://github.com/andrewjpage))
	920	- 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))
	921	- print fragment blocks [\#55](https://github.com/sanger-pathogens/Roary/pull/55) ([andrewjpage](https://github.com/andrewjpage))
	922	- Fix ordering of accessory [\#54](https://github.com/sanger-pathogens/Roary/pull/54) ([andrewjpage](https://github.com/andrewjpage))
	923	- fix r plots [\#53](https://github.com/sanger-pathogens/Roary/pull/53) ([andrewjpage](https://github.com/andrewjpage))
	924	- Overlapping proteins [\#52](https://github.com/sanger-pathogens/Roary/pull/52) ([andrewjpage](https://github.com/andrewjpage))
	925	- Gene order [\#51](https://github.com/sanger-pathogens/Roary/pull/51) ([andrewjpage](https://github.com/andrewjpage))
	926	- pass job runner to iterative cdhit [\#50](https://github.com/sanger-pathogens/Roary/pull/50) ([andrewjpage](https://github.com/andrewjpage))
	927	- iterative cdhit in a job [\#49](https://github.com/sanger-pathogens/Roary/pull/49) ([andrewjpage](https://github.com/andrewjpage))
	928	- Fix tests [\#48](https://github.com/sanger-pathogens/Roary/pull/48) ([andrewjpage](https://github.com/andrewjpage))
	929	- Prefilter optimisation [\#47](https://github.com/sanger-pathogens/Roary/pull/47) ([andrewjpage](https://github.com/andrewjpage))
	930	- dont split groups [\#46](https://github.com/sanger-pathogens/Roary/pull/46) ([andrewjpage](https://github.com/andrewjpage))
	931	- rename create plots R script [\#45](https://github.com/sanger-pathogens/Roary/pull/45) ([andrewjpage](https://github.com/andrewjpage))
	932	- cdhit should output full description of sequence name [\#44](https://github.com/sanger-pathogens/Roary/pull/44) ([andrewjpage](https://github.com/andrewjpage))
	933	- Gene count plot [\#43](https://github.com/sanger-pathogens/Roary/pull/43) ([andrewjpage](https://github.com/andrewjpage))
	934	- align gene multifasta files using muscle [\#42](https://github.com/sanger-pathogens/Roary/pull/42) ([andrewjpage](https://github.com/andrewjpage))
	935	- Reorder spreadsheet [\#41](https://github.com/sanger-pathogens/Roary/pull/41) ([andrewjpage](https://github.com/andrewjpage))
	936	- Reorder spreadsheet [\#40](https://github.com/sanger-pathogens/Roary/pull/40) ([andrewjpage](https://github.com/andrewjpage))
	937	- Speedup post analysis [\#39](https://github.com/sanger-pathogens/Roary/pull/39) ([andrewjpage](https://github.com/andrewjpage))
	938	- Presence and absence of genes [\#38](https://github.com/sanger-pathogens/Roary/pull/38) ([andrewjpage](https://github.com/andrewjpage))
	939	- split big groups based on annotation [\#37](https://github.com/sanger-pathogens/Roary/pull/37) ([andrewjpage](https://github.com/andrewjpage))
	940	- make multifasta files easier to sort [\#36](https://github.com/sanger-pathogens/Roary/pull/36) ([andrewjpage](https://github.com/andrewjpage))
	941	- dont wait in lfs scheduler [\#35](https://github.com/sanger-pathogens/Roary/pull/35) ([andrewjpage](https://github.com/andrewjpage))
	942	- run post analysis as a job [\#34](https://github.com/sanger-pathogens/Roary/pull/34) ([andrewjpage](https://github.com/andrewjpage))
	943	- annotate the names of the groups files [\#33](https://github.com/sanger-pathogens/Roary/pull/33) ([andrewjpage](https://github.com/andrewjpage))
	944	- Output all sequences making up pan genome in multifasta files [\#32](https://github.com/sanger-pathogens/Roary/pull/32) ([andrewjpage](https://github.com/andrewjpage))
	945	- Run external applications through lsf [\#31](https://github.com/sanger-pathogens/Roary/pull/31) ([andrewjpage](https://github.com/andrewjpage))
	946	- remove done dependancy job [\#30](https://github.com/sanger-pathogens/Roary/pull/30) ([andrewjpage](https://github.com/andrewjpage))
	947	- blocking job [\#29](https://github.com/sanger-pathogens/Roary/pull/29) ([andrewjpage](https://github.com/andrewjpage))
	948	- Filter unknowns in LSF jobs [\#28](https://github.com/sanger-pathogens/Roary/pull/28) ([andrewjpage](https://github.com/andrewjpage))
	949	- Pass job runner through to extract gffs [\#27](https://github.com/sanger-pathogens/Roary/pull/27) ([andrewjpage](https://github.com/andrewjpage))
	950	- Change case of GFF commandline class [\#26](https://github.com/sanger-pathogens/Roary/pull/26) ([andrewjpage](https://github.com/andrewjpage))
	951	- use LSF to do the inital parsing of input files [\#25](https://github.com/sanger-pathogens/Roary/pull/25) ([andrewjpage](https://github.com/andrewjpage))
	952	- renamed LICENSE [\#24](https://github.com/sanger-pathogens/Roary/pull/24) ([CraigPorter](https://github.com/CraigPorter))
	953	- GPL [\#23](https://github.com/sanger-pathogens/Roary/pull/23) ([andrewjpage](https://github.com/andrewjpage))
	954	- lsf memory in mb [\#22](https://github.com/sanger-pathogens/Roary/pull/22) ([andrewjpage](https://github.com/andrewjpage))
	955	- low complexity filtering [\#21](https://github.com/sanger-pathogens/Roary/pull/21) ([andrewjpage](https://github.com/andrewjpage))
	956	- inflate clusters where the representative gene is not the first [\#20](https://github.com/sanger-pathogens/Roary/pull/20) ([andrewjpage](https://github.com/andrewjpage))
	957	- report more sequences from blastp [\#19](https://github.com/sanger-pathogens/Roary/pull/19) ([andrewjpage](https://github.com/andrewjpage))
	958	- update tests for different input processing [\#18](https://github.com/sanger-pathogens/Roary/pull/18) ([andrewjpage](https://github.com/andrewjpage))
	959	- speedup extracting proteins from gff [\#17](https://github.com/sanger-pathogens/Roary/pull/17) ([andrewjpage](https://github.com/andrewjpage))
	960	- sort spreadsheet by number of isolates [\#16](https://github.com/sanger-pathogens/Roary/pull/16) ([andrewjpage](https://github.com/andrewjpage))
	961	- create spreadsheets of differences between sets [\#15](https://github.com/sanger-pathogens/Roary/pull/15) ([andrewjpage](https://github.com/andrewjpage))
	962	- Output statistics on groups [\#14](https://github.com/sanger-pathogens/Roary/pull/14) ([andrewjpage](https://github.com/andrewjpage))
	963	- Find the difference between isolates [\#13](https://github.com/sanger-pathogens/Roary/pull/13) ([andrewjpage](https://github.com/andrewjpage))
	964	- check if group is null [\#12](https://github.com/sanger-pathogens/Roary/pull/12) ([andrewjpage](https://github.com/andrewjpage))
	965	- catch undef [\#11](https://github.com/sanger-pathogens/Roary/pull/11) ([andrewjpage](https://github.com/andrewjpage))
	966	- tests for create pan genome script [\#10](https://github.com/sanger-pathogens/Roary/pull/10) ([andrewjpage](https://github.com/andrewjpage))
	967	- label fasta sequences with annotation ID [\#9](https://github.com/sanger-pathogens/Roary/pull/9) ([andrewjpage](https://github.com/andrewjpage))
	968	- 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))
	969	- transfer annotation [\#7](https://github.com/sanger-pathogens/Roary/pull/7) ([andrewjpage](https://github.com/andrewjpage))
	970	- speedup searching fastas [\#6](https://github.com/sanger-pathogens/Roary/pull/6) ([andrewjpage](https://github.com/andrewjpage))
	971	- typo in memory estimation [\#5](https://github.com/sanger-pathogens/Roary/pull/5) ([andrewjpage](https://github.com/andrewjpage))
	972	- run mcl and inflate results [\#4](https://github.com/sanger-pathogens/Roary/pull/4) ([andrewjpage](https://github.com/andrewjpage))
	973	- vary memory usage according to input file size [\#3](https://github.com/sanger-pathogens/Roary/pull/3) ([andrewjpage](https://github.com/andrewjpage))
	974	- working on real data [\#2](https://github.com/sanger-pathogens/Roary/pull/2) ([andrewjpage](https://github.com/andrewjpage))
	975	- Initial functionality [\#1](https://github.com/sanger-pathogens/Roary/pull/1) ([andrewjpage](https://github.com/andrewjpage))
	976