roary_plots: Roary/CHANGELOG.md annotate

annotate Roary/CHANGELOG.md @ 2:3f98630a0c20 draft

Deleted selected files

author	dereeper
date	Fri, 12 Nov 2021 16:30:50 +0000
parents	c47a5f61bc9f
children

rev	line source
0 c47a5f61bc9f Uploaded dereeper parents: diff changeset	1 # Change Log
c47a5f61bc9f Uploaded dereeper parents: diff changeset	2
c47a5f61bc9f Uploaded dereeper parents: diff changeset	3 ## [Unreleased](https://github.com/sanger-pathogens/Roary/tree/HEAD)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	4
c47a5f61bc9f Uploaded dereeper parents: diff changeset	5 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.12.0...HEAD)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	6
c47a5f61bc9f Uploaded dereeper parents: diff changeset	7 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	8
c47a5f61bc9f Uploaded dereeper parents: diff changeset	9 - Feature Request: Clear error message for duplicated file names [\#363](https://github.com/sanger-pathogens/Roary/issues/363)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	10
c47a5f61bc9f Uploaded dereeper parents: diff changeset	11 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	12
c47a5f61bc9f Uploaded dereeper parents: diff changeset	13 - uninitialized value warning [\#297](https://github.com/sanger-pathogens/Roary/issues/297)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	14 - 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)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	15
c47a5f61bc9f Uploaded dereeper parents: diff changeset	16 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	17
c47a5f61bc9f Uploaded dereeper parents: diff changeset	18 - Interpretation accessory\_binary\_genes newick [\#429](https://github.com/sanger-pathogens/Roary/issues/429)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	19 - No gene annotation in gene\_presence\_absence.csv output [\#428](https://github.com/sanger-pathogens/Roary/issues/428)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	20 - Compilation aborted at pan\_genome\_post\_analysis [\#427](https://github.com/sanger-pathogens/Roary/issues/427)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	21 - Could not obtain pan\_genome\_sequences [\#426](https://github.com/sanger-pathogens/Roary/issues/426)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	22 - Pan genome for fungal genomes [\#425](https://github.com/sanger-pathogens/Roary/issues/425)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	23 - multifasta for all proteins [\#424](https://github.com/sanger-pathogens/Roary/issues/424)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	24 - roary\_plots.py KeyError: "X" not in index [\#423](https://github.com/sanger-pathogens/Roary/issues/423)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	25 - Confirm that use of BLAST's `-max\_target\_seqs` is intentional [\#422](https://github.com/sanger-pathogens/Roary/issues/422)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	26 - query\_pan\_genome 'Cant access file' error $Non-Working-Directory inputs$ [\#421](https://github.com/sanger-pathogens/Roary/issues/421)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	27 - How many .gff files does Roary need? [\#419](https://github.com/sanger-pathogens/Roary/issues/419)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	28 - Installation through Bioconda not working [\#418](https://github.com/sanger-pathogens/Roary/issues/418)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	29 - Is it possible to run roary without prokka output files? [\#417](https://github.com/sanger-pathogens/Roary/issues/417)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	30 - Exiting early because number of clusters is too high [\#415](https://github.com/sanger-pathogens/Roary/issues/415)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	31 - MSG: Got a sequence without letters. Could not guess alphabet? [\#414](https://github.com/sanger-pathogens/Roary/issues/414)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	32 - 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)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	33 - issues with running and empty files [\#411](https://github.com/sanger-pathogens/Roary/issues/411)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	34 - MSG: Got a sequence without letters. Could not guess alphabet [\#410](https://github.com/sanger-pathogens/Roary/issues/410)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	35 - moose.pm issue [\#407](https://github.com/sanger-pathogens/Roary/issues/407)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	36 - Tutorial data: extract\_proteome\_from\_gff [\#406](https://github.com/sanger-pathogens/Roary/issues/406)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	37 - Tutorial data: extract\_proteome\_from\_gff [\#403](https://github.com/sanger-pathogens/Roary/issues/403)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	38 - gene\_presence\_absence.csv incomplete [\#402](https://github.com/sanger-pathogens/Roary/issues/402)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	39 - Roary including non-protein coding features? [\#398](https://github.com/sanger-pathogens/Roary/issues/398)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	40 - Question: what programs can be used to visualize embl and dot files? [\#394](https://github.com/sanger-pathogens/Roary/issues/394)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	41 - Roary Does not terminated successfully [\#388](https://github.com/sanger-pathogens/Roary/issues/388)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	42 - python: can't open file 'roary\_plots.py': \[Errno 2\] No such file or directory [\#385](https://github.com/sanger-pathogens/Roary/issues/385)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	43 - Roary does not finish analysis even though cluster job queue returns successful completion [\#383](https://github.com/sanger-pathogens/Roary/issues/383)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	44 - Genes $well$ annotated in prokka end up all in different groups?? [\#355](https://github.com/sanger-pathogens/Roary/issues/355)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	45 - could not determine version of cd-hit [\#322](https://github.com/sanger-pathogens/Roary/issues/322)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	46 - Use of uninitialized value in require at $eval 792$ line 1. [\#308](https://github.com/sanger-pathogens/Roary/issues/308)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	47 - Error: unexpected input in "\_" [\#299](https://github.com/sanger-pathogens/Roary/issues/299)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	48 - inconsistent referencing of $TMPDIR ? [\#287](https://github.com/sanger-pathogens/Roary/issues/287)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	49
c47a5f61bc9f Uploaded dereeper parents: diff changeset	50 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	51
c47a5f61bc9f Uploaded dereeper parents: diff changeset	52 - Include tests in README [\#430](https://github.com/sanger-pathogens/Roary/pull/430) ([ssjunnebo](https://github.com/ssjunnebo))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	53 - 621556 badges [\#420](https://github.com/sanger-pathogens/Roary/pull/420) ([ssjunnebo](https://github.com/ssjunnebo))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	54 - Update roary\_plots from .ix to .loc [\#416](https://github.com/sanger-pathogens/Roary/pull/416) ([EvdH0](https://github.com/EvdH0))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	55 - Use only CDS features from GFF [\#400](https://github.com/sanger-pathogens/Roary/pull/400) ([embatty](https://github.com/embatty))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	56 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	57 - Avoid deprecation errors in roary\_plots [\#389](https://github.com/sanger-pathogens/Roary/pull/389) ([mgalardini](https://github.com/mgalardini))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	58
c47a5f61bc9f Uploaded dereeper parents: diff changeset	59 ## [v3.12.0](https://github.com/sanger-pathogens/Roary/tree/v3.12.0) (2018-01-23)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	60 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.4...v3.12.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	61
c47a5f61bc9f Uploaded dereeper parents: diff changeset	62 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	63
c47a5f61bc9f Uploaded dereeper parents: diff changeset	64 - Reduce min gene size [\#384](https://github.com/sanger-pathogens/Roary/pull/384) ([ssjunnebo](https://github.com/ssjunnebo))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	65
c47a5f61bc9f Uploaded dereeper parents: diff changeset	66 ## [v3.11.4](https://github.com/sanger-pathogens/Roary/tree/v3.11.4) (2018-01-16)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	67 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.3...v3.11.4)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	68
c47a5f61bc9f Uploaded dereeper parents: diff changeset	69 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	70
c47a5f61bc9f Uploaded dereeper parents: diff changeset	71 - Roary seemed to have stopped prematurely; any way to continue the run? [\#380](https://github.com/sanger-pathogens/Roary/issues/380)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	72 - Getting prank version without the online check [\#377](https://github.com/sanger-pathogens/Roary/issues/377)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	73 - Kraken version parsing error: [\#376](https://github.com/sanger-pathogens/Roary/issues/376)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	74 - 3.11.1 failing 2/55 $3/791$ tests [\#375](https://github.com/sanger-pathogens/Roary/issues/375)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	75 - Fix for prank version check [\#361](https://github.com/sanger-pathogens/Roary/issues/361)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	76 - mafft version check still failing - bug in regexp found [\#360](https://github.com/sanger-pathogens/Roary/issues/360)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	77 - roary -a =\> Use of uninitialized value in concatenation $.$ [\#270](https://github.com/sanger-pathogens/Roary/issues/270)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	78
c47a5f61bc9f Uploaded dereeper parents: diff changeset	79 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	80
c47a5f61bc9f Uploaded dereeper parents: diff changeset	81 - Fix dependancy checking option [\#382](https://github.com/sanger-pathogens/Roary/pull/382) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	82
c47a5f61bc9f Uploaded dereeper parents: diff changeset	83 ## [v3.11.3](https://github.com/sanger-pathogens/Roary/tree/v3.11.3) (2018-01-12)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	84 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.2...v3.11.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	85
c47a5f61bc9f Uploaded dereeper parents: diff changeset	86 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	87
c47a5f61bc9f Uploaded dereeper parents: diff changeset	88 - Version fix [\#379](https://github.com/sanger-pathogens/Roary/pull/379) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	89
c47a5f61bc9f Uploaded dereeper parents: diff changeset	90 ## [v3.11.2](https://github.com/sanger-pathogens/Roary/tree/v3.11.2) (2018-01-12)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	91 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.1...v3.11.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	92
c47a5f61bc9f Uploaded dereeper parents: diff changeset	93 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	94
c47a5f61bc9f Uploaded dereeper parents: diff changeset	95 - ExtractProteomeFromGff.t failing tests 3.11.0 [\#373](https://github.com/sanger-pathogens/Roary/issues/373)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	96
c47a5f61bc9f Uploaded dereeper parents: diff changeset	97 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	98
c47a5f61bc9f Uploaded dereeper parents: diff changeset	99 - fix mafft and kraken version extraction [\#378](https://github.com/sanger-pathogens/Roary/pull/378) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	100
c47a5f61bc9f Uploaded dereeper parents: diff changeset	101 ## [v3.11.1](https://github.com/sanger-pathogens/Roary/tree/v3.11.1) (2018-01-10)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	102 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.11.0...v3.11.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	103
c47a5f61bc9f Uploaded dereeper parents: diff changeset	104 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	105
c47a5f61bc9f Uploaded dereeper parents: diff changeset	106 - Sorting in version 3.11.0: uppercase letters first, lowercase second $non-alphabetical$ [\#371](https://github.com/sanger-pathogens/Roary/issues/371)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	107 - Genbank input [\#365](https://github.com/sanger-pathogens/Roary/issues/365)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	108 - not all annotated features are allocated to the clusters [\#359](https://github.com/sanger-pathogens/Roary/issues/359)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	109
c47a5f61bc9f Uploaded dereeper parents: diff changeset	110 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	111
c47a5f61bc9f Uploaded dereeper parents: diff changeset	112 - Bedtools getfasta format fix [\#374](https://github.com/sanger-pathogens/Roary/pull/374) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	113 - Update roary\_plots.py [\#372](https://github.com/sanger-pathogens/Roary/pull/372) ([franz89](https://github.com/franz89))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	114 - Issue \#363 add check for duplicate basenames [\#370](https://github.com/sanger-pathogens/Roary/pull/370) ([nickp60](https://github.com/nickp60))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	115 - README.md: Update Guix install instructions. [\#362](https://github.com/sanger-pathogens/Roary/pull/362) ([wwood](https://github.com/wwood))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	116
c47a5f61bc9f Uploaded dereeper parents: diff changeset	117 ## [v3.11.0](https://github.com/sanger-pathogens/Roary/tree/v3.11.0) (2017-10-10)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	118 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.2...v3.11.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	119
c47a5f61bc9f Uploaded dereeper parents: diff changeset	120 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	121
c47a5f61bc9f Uploaded dereeper parents: diff changeset	122 - Can't get version of kraken, kraken-report or mafft ? [\#312](https://github.com/sanger-pathogens/Roary/issues/312)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	123
c47a5f61bc9f Uploaded dereeper parents: diff changeset	124 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	125
c47a5f61bc9f Uploaded dereeper parents: diff changeset	126 - number\_of\_conserved\_genes.Rtab [\#354](https://github.com/sanger-pathogens/Roary/issues/354)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	127 - \[question\] Should it take this long? [\#352](https://github.com/sanger-pathogens/Roary/issues/352)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	128
c47a5f61bc9f Uploaded dereeper parents: diff changeset	129 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	130
c47a5f61bc9f Uploaded dereeper parents: diff changeset	131 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	132
c47a5f61bc9f Uploaded dereeper parents: diff changeset	133 ## [v3.10.2](https://github.com/sanger-pathogens/Roary/tree/v3.10.2) (2017-09-08)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	134 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.1...v3.10.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	135
c47a5f61bc9f Uploaded dereeper parents: diff changeset	136 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	137
c47a5f61bc9f Uploaded dereeper parents: diff changeset	138 - \[version 3.8.0\] Roary crashes at end on perl error message [\#323](https://github.com/sanger-pathogens/Roary/issues/323)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	139 - Cant open file: \_accessory\_clusters.clstr [\#320](https://github.com/sanger-pathogens/Roary/issues/320)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	140
c47a5f61bc9f Uploaded dereeper parents: diff changeset	141 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	142
c47a5f61bc9f Uploaded dereeper parents: diff changeset	143 - get kraken version [\#351](https://github.com/sanger-pathogens/Roary/pull/351) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	144
c47a5f61bc9f Uploaded dereeper parents: diff changeset	145 ## [v3.10.1](https://github.com/sanger-pathogens/Roary/tree/v3.10.1) (2017-09-07)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	146 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.10.0...v3.10.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	147
c47a5f61bc9f Uploaded dereeper parents: diff changeset	148 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	149
c47a5f61bc9f Uploaded dereeper parents: diff changeset	150 - Auto-detect if input files are GFF or FASTA [\#348](https://github.com/sanger-pathogens/Roary/issues/348)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	151 - Can "Fixing input GFF files" be parallelized? [\#342](https://github.com/sanger-pathogens/Roary/issues/342)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	152
c47a5f61bc9f Uploaded dereeper parents: diff changeset	153 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	154
c47a5f61bc9f Uploaded dereeper parents: diff changeset	155 - The GNU General Public License, Version not specified [\#344](https://github.com/sanger-pathogens/Roary/issues/344)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	156
c47a5f61bc9f Uploaded dereeper parents: diff changeset	157 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	158
c47a5f61bc9f Uploaded dereeper parents: diff changeset	159 - MSG: The sequence does not appear to be FASTA format $lacks a descriptor line '\>'$ [\#346](https://github.com/sanger-pathogens/Roary/issues/346)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	160
c47a5f61bc9f Uploaded dereeper parents: diff changeset	161 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	162
c47a5f61bc9f Uploaded dereeper parents: diff changeset	163 - Improve input file handling [\#350](https://github.com/sanger-pathogens/Roary/pull/350) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	164
c47a5f61bc9f Uploaded dereeper parents: diff changeset	165 ## [v3.10.0](https://github.com/sanger-pathogens/Roary/tree/v3.10.0) (2017-09-07)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	166 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.1...v3.10.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	167
c47a5f61bc9f Uploaded dereeper parents: diff changeset	168 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	169
c47a5f61bc9f Uploaded dereeper parents: diff changeset	170 - Use of uninitialized value $Perl$ [\#345](https://github.com/sanger-pathogens/Roary/issues/345)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	171 - identical .gff file names from different genome, and then issue with mcl groups [\#341](https://github.com/sanger-pathogens/Roary/issues/341)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	172 - Cant open file: \_clustered.clstr [\#339](https://github.com/sanger-pathogens/Roary/issues/339)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	173
c47a5f61bc9f Uploaded dereeper parents: diff changeset	174 ## [v3.9.1](https://github.com/sanger-pathogens/Roary/tree/v3.9.1) (2017-08-22)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	175 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.9.0...v3.9.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	176
c47a5f61bc9f Uploaded dereeper parents: diff changeset	177 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	178
c47a5f61bc9f Uploaded dereeper parents: diff changeset	179 - Optionally allow paralogs in core gene alignment [\#343](https://github.com/sanger-pathogens/Roary/pull/343) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	180 - Script to find frequency of unique genes in samples [\#340](https://github.com/sanger-pathogens/Roary/pull/340) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	181
c47a5f61bc9f Uploaded dereeper parents: diff changeset	182 ## [v3.9.0](https://github.com/sanger-pathogens/Roary/tree/v3.9.0) (2017-08-09)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	183 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.2...v3.9.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	184
c47a5f61bc9f Uploaded dereeper parents: diff changeset	185 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	186
c47a5f61bc9f Uploaded dereeper parents: diff changeset	187 - roary\_plots: pangenome matrix tree does not look like input.newick tree [\#333](https://github.com/sanger-pathogens/Roary/issues/333)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	188 - use Roary with RAST files [\#332](https://github.com/sanger-pathogens/Roary/issues/332)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	189 - Roary [\#329](https://github.com/sanger-pathogens/Roary/issues/329)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	190 - sampling number is 10 in number of genes in pan and core genome [\#319](https://github.com/sanger-pathogens/Roary/issues/319)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	191
c47a5f61bc9f Uploaded dereeper parents: diff changeset	192 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	193
c47a5f61bc9f Uploaded dereeper parents: diff changeset	194 - Grammar edits [\#327](https://github.com/sanger-pathogens/Roary/pull/327) ([cgreene](https://github.com/cgreene))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	195 - allow for inflation factor for MCL to be changed [\#326](https://github.com/sanger-pathogens/Roary/pull/326) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	196
c47a5f61bc9f Uploaded dereeper parents: diff changeset	197 ## [v3.8.2](https://github.com/sanger-pathogens/Roary/tree/v3.8.2) (2017-05-21)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	198 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.1...v3.8.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	199
c47a5f61bc9f Uploaded dereeper parents: diff changeset	200 ## [v3.8.1](https://github.com/sanger-pathogens/Roary/tree/v3.8.1) (2017-05-21)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	201 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.8.0...v3.8.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	202
c47a5f61bc9f Uploaded dereeper parents: diff changeset	203 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	204
c47a5f61bc9f Uploaded dereeper parents: diff changeset	205 - BLAST Database error [\#321](https://github.com/sanger-pathogens/Roary/issues/321)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	206 - Results for same input differ always a bit $summary\_statistics.txt$ [\#318](https://github.com/sanger-pathogens/Roary/issues/318)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	207 - Error: Couldnt open GFF file [\#314](https://github.com/sanger-pathogens/Roary/issues/314)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	208 - Help with query\_pan\_genome [\#313](https://github.com/sanger-pathogens/Roary/issues/313)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	209
c47a5f61bc9f Uploaded dereeper parents: diff changeset	210 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	211
c47a5f61bc9f Uploaded dereeper parents: diff changeset	212 - update email address [\#325](https://github.com/sanger-pathogens/Roary/pull/325) ([ssjunnebo](https://github.com/ssjunnebo))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	213 - New option to roary\_plots.py [\#317](https://github.com/sanger-pathogens/Roary/pull/317) ([mgalardini](https://github.com/mgalardini))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	214
c47a5f61bc9f Uploaded dereeper parents: diff changeset	215 ## [v3.8.0](https://github.com/sanger-pathogens/Roary/tree/v3.8.0) (2017-01-25)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	216 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.1...v3.8.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	217
c47a5f61bc9f Uploaded dereeper parents: diff changeset	218 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	219
c47a5f61bc9f Uploaded dereeper parents: diff changeset	220 - Old version in the master tarball? [\#300](https://github.com/sanger-pathogens/Roary/issues/300)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	221 - prank is not installed $Linuxbrew$ [\#294](https://github.com/sanger-pathogens/Roary/issues/294)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	222 - roary\_plots.py problem [\#292](https://github.com/sanger-pathogens/Roary/issues/292)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	223
c47a5f61bc9f Uploaded dereeper parents: diff changeset	224 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	225
c47a5f61bc9f Uploaded dereeper parents: diff changeset	226 - Support latest version of blast [\#306](https://github.com/sanger-pathogens/Roary/pull/306) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	227 - infgen [\#305](https://github.com/sanger-pathogens/Roary/pull/305) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	228 - update from 108 to 118 [\#304](https://github.com/sanger-pathogens/Roary/pull/304) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	229 - update usage text for iterative CD-hit [\#301](https://github.com/sanger-pathogens/Roary/pull/301) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	230
c47a5f61bc9f Uploaded dereeper parents: diff changeset	231 ## [v3.7.1](https://github.com/sanger-pathogens/Roary/tree/v3.7.1) (2016-11-01)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	232 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.7.0...v3.7.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	233
c47a5f61bc9f Uploaded dereeper parents: diff changeset	234 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	235
c47a5f61bc9f Uploaded dereeper parents: diff changeset	236 - core\_gene\_alignment.aln missing [\#284](https://github.com/sanger-pathogens/Roary/issues/284)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	237 - Is these results fine to use? [\#282](https://github.com/sanger-pathogens/Roary/issues/282)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	238
c47a5f61bc9f Uploaded dereeper parents: diff changeset	239 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	240
c47a5f61bc9f Uploaded dereeper parents: diff changeset	241 - fix spelling [\#280](https://github.com/sanger-pathogens/Roary/pull/280) ([satta](https://github.com/satta))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	242 - dont add POD to end of R scripts [\#279](https://github.com/sanger-pathogens/Roary/pull/279) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	243
c47a5f61bc9f Uploaded dereeper parents: diff changeset	244 ## [v3.7.0](https://github.com/sanger-pathogens/Roary/tree/v3.7.0) (2016-09-23)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	245 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.9...v3.7.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	246
c47a5f61bc9f Uploaded dereeper parents: diff changeset	247 ## [v3.6.9](https://github.com/sanger-pathogens/Roary/tree/v3.6.9) (2016-09-22)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	248 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.8...v3.6.9)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	249
c47a5f61bc9f Uploaded dereeper parents: diff changeset	250 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	251
c47a5f61bc9f Uploaded dereeper parents: diff changeset	252 - I have published a Roary homebrew formula [\#208](https://github.com/sanger-pathogens/Roary/issues/208)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	253 - Getting Roary into Homebrew [\#152](https://github.com/sanger-pathogens/Roary/issues/152)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	254
c47a5f61bc9f Uploaded dereeper parents: diff changeset	255 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	256
c47a5f61bc9f Uploaded dereeper parents: diff changeset	257 - roary\_plots.py missing [\#277](https://github.com/sanger-pathogens/Roary/issues/277)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	258 - Errors when downloaded sequences from NCBI [\#274](https://github.com/sanger-pathogens/Roary/issues/274)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	259 - Same dataset different results! [\#271](https://github.com/sanger-pathogens/Roary/issues/271)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	260 - \_clustered.clstr file does not exist, cannot be read [\#250](https://github.com/sanger-pathogens/Roary/issues/250)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	261
c47a5f61bc9f Uploaded dereeper parents: diff changeset	262 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	263
c47a5f61bc9f Uploaded dereeper parents: diff changeset	264 - Fixed easy-init warnings - 529655 [\#278](https://github.com/sanger-pathogens/Roary/pull/278) ([psweston](https://github.com/psweston))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	265 - README.md: Add instructions for GNU Guix. [\#273](https://github.com/sanger-pathogens/Roary/pull/273) ([wwood](https://github.com/wwood))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	266
c47a5f61bc9f Uploaded dereeper parents: diff changeset	267 ## [v3.6.8](https://github.com/sanger-pathogens/Roary/tree/v3.6.8) (2016-08-02)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	268 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.7...v3.6.8)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	269
c47a5f61bc9f Uploaded dereeper parents: diff changeset	270 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	271
c47a5f61bc9f Uploaded dereeper parents: diff changeset	272 - Allow gene names from gb [\#266](https://github.com/sanger-pathogens/Roary/pull/266) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	273 - Missing genes [\#265](https://github.com/sanger-pathogens/Roary/pull/265) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	274
c47a5f61bc9f Uploaded dereeper parents: diff changeset	275 ## [v3.6.7](https://github.com/sanger-pathogens/Roary/tree/v3.6.7) (2016-07-26)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	276 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.6...v3.6.7)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	277
c47a5f61bc9f Uploaded dereeper parents: diff changeset	278 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	279
c47a5f61bc9f Uploaded dereeper parents: diff changeset	280 - 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)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	281 - roary R plots don't work on server --- lack of X11 [\#194](https://github.com/sanger-pathogens/Roary/issues/194)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	282
c47a5f61bc9f Uploaded dereeper parents: diff changeset	283 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	284
c47a5f61bc9f Uploaded dereeper parents: diff changeset	285 - empty accessory\_binary\_genes.fa file [\#262](https://github.com/sanger-pathogens/Roary/issues/262)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	286 - a guix package [\#259](https://github.com/sanger-pathogens/Roary/issues/259)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	287 - create\_pan\_genome\_plots.R - X11 font problem [\#230](https://github.com/sanger-pathogens/Roary/issues/230)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	288 - Roary not generating pan\_genome\_reference.fa [\#223](https://github.com/sanger-pathogens/Roary/issues/223)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	289 - Roary not using packaged executables [\#215](https://github.com/sanger-pathogens/Roary/issues/215)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	290
c47a5f61bc9f Uploaded dereeper parents: diff changeset	291 ## [v3.6.6](https://github.com/sanger-pathogens/Roary/tree/v3.6.6) (2016-07-25)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	292 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.5...v3.6.6)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	293
c47a5f61bc9f Uploaded dereeper parents: diff changeset	294 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	295
c47a5f61bc9f Uploaded dereeper parents: diff changeset	296 - GFF parsing doesn't match GFF3 specification [\#249](https://github.com/sanger-pathogens/Roary/issues/249)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	297
c47a5f61bc9f Uploaded dereeper parents: diff changeset	298 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	299
c47a5f61bc9f Uploaded dereeper parents: diff changeset	300 - Fix empty accessory binary [\#264](https://github.com/sanger-pathogens/Roary/pull/264) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	301 - change to dist zilla starter bundle [\#261](https://github.com/sanger-pathogens/Roary/pull/261) ([nds](https://github.com/nds))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	302
c47a5f61bc9f Uploaded dereeper parents: diff changeset	303 ## [v3.6.5](https://github.com/sanger-pathogens/Roary/tree/v3.6.5) (2016-07-20)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	304 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.4...v3.6.5)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	305
c47a5f61bc9f Uploaded dereeper parents: diff changeset	306 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	307
c47a5f61bc9f Uploaded dereeper parents: diff changeset	308 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	309 - catch divide by zero error [\#258](https://github.com/sanger-pathogens/Roary/pull/258) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	310
c47a5f61bc9f Uploaded dereeper parents: diff changeset	311 ## [v3.6.4](https://github.com/sanger-pathogens/Roary/tree/v3.6.4) (2016-07-06)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	312 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.3...v3.6.4)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	313
c47a5f61bc9f Uploaded dereeper parents: diff changeset	314 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	315
c47a5f61bc9f Uploaded dereeper parents: diff changeset	316 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	317
c47a5f61bc9f Uploaded dereeper parents: diff changeset	318 ## [v3.6.3](https://github.com/sanger-pathogens/Roary/tree/v3.6.3) (2016-07-01)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	319 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.2...v3.6.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	320
c47a5f61bc9f Uploaded dereeper parents: diff changeset	321 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	322
c47a5f61bc9f Uploaded dereeper parents: diff changeset	323 - Speed up alignments [\#256](https://github.com/sanger-pathogens/Roary/pull/256) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	324
c47a5f61bc9f Uploaded dereeper parents: diff changeset	325 ## [v3.6.2](https://github.com/sanger-pathogens/Roary/tree/v3.6.2) (2016-05-10)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	326 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.1...v3.6.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	327
c47a5f61bc9f Uploaded dereeper parents: diff changeset	328 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	329
c47a5f61bc9f Uploaded dereeper parents: diff changeset	330 - Prefix utility commands with roary- ? [\#226](https://github.com/sanger-pathogens/Roary/issues/226)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	331
c47a5f61bc9f Uploaded dereeper parents: diff changeset	332 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	333
c47a5f61bc9f Uploaded dereeper parents: diff changeset	334 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	335 - get rid of warning message [\#246](https://github.com/sanger-pathogens/Roary/pull/246) ([satta](https://github.com/satta))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	336
c47a5f61bc9f Uploaded dereeper parents: diff changeset	337 ## [v3.6.1](https://github.com/sanger-pathogens/Roary/tree/v3.6.1) (2016-04-18)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	338 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.6.0...v3.6.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	339
c47a5f61bc9f Uploaded dereeper parents: diff changeset	340 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	341
c47a5f61bc9f Uploaded dereeper parents: diff changeset	342 - roary\_plots.py generating flawed plots [\#221](https://github.com/sanger-pathogens/Roary/issues/221)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	343
c47a5f61bc9f Uploaded dereeper parents: diff changeset	344 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	345
c47a5f61bc9f Uploaded dereeper parents: diff changeset	346 - Core gene file missing error [\#241](https://github.com/sanger-pathogens/Roary/issues/241)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	347
c47a5f61bc9f Uploaded dereeper parents: diff changeset	348 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	349
c47a5f61bc9f Uploaded dereeper parents: diff changeset	350 - prefix commands with roary [\#244](https://github.com/sanger-pathogens/Roary/pull/244) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	351 - More improvements to roary\_plots [\#240](https://github.com/sanger-pathogens/Roary/pull/240) ([mgalardini](https://github.com/mgalardini))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	352
c47a5f61bc9f Uploaded dereeper parents: diff changeset	353 ## [v3.6.0](https://github.com/sanger-pathogens/Roary/tree/v3.6.0) (2016-02-23)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	354 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.9...v3.6.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	355
c47a5f61bc9f Uploaded dereeper parents: diff changeset	356 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	357
c47a5f61bc9f Uploaded dereeper parents: diff changeset	358 - MSG: Got a sequence without letters. Could not guess alphabet [\#229](https://github.com/sanger-pathogens/Roary/issues/229)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	359
c47a5f61bc9f Uploaded dereeper parents: diff changeset	360 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	361
c47a5f61bc9f Uploaded dereeper parents: diff changeset	362 - 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)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	363 - How to use multiple switches in commandline? [\#232](https://github.com/sanger-pathogens/Roary/issues/232)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	364
c47a5f61bc9f Uploaded dereeper parents: diff changeset	365 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	366
c47a5f61bc9f Uploaded dereeper parents: diff changeset	367 - Improvements to roary\_plots [\#236](https://github.com/sanger-pathogens/Roary/pull/236) ([mgalardini](https://github.com/mgalardini))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	368 - Rollback 3 5 8 [\#235](https://github.com/sanger-pathogens/Roary/pull/235) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	369
c47a5f61bc9f Uploaded dereeper parents: diff changeset	370 ## [v3.5.9](https://github.com/sanger-pathogens/Roary/tree/v3.5.9) (2016-02-17)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	371 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.8...v3.5.9)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	372
c47a5f61bc9f Uploaded dereeper parents: diff changeset	373 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	374
c47a5f61bc9f Uploaded dereeper parents: diff changeset	375 - What clusters end up in gene accessory\_binary\_genes.fa ? [\#225](https://github.com/sanger-pathogens/Roary/issues/225)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	376
c47a5f61bc9f Uploaded dereeper parents: diff changeset	377 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	378
c47a5f61bc9f Uploaded dereeper parents: diff changeset	379 - roary.github.io just prints HELLO [\#233](https://github.com/sanger-pathogens/Roary/issues/233)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	380
c47a5f61bc9f Uploaded dereeper parents: diff changeset	381 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	382
c47a5f61bc9f Uploaded dereeper parents: diff changeset	383 - Fix minor typo [\#231](https://github.com/sanger-pathogens/Roary/pull/231) ([abremges](https://github.com/abremges))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	384
c47a5f61bc9f Uploaded dereeper parents: diff changeset	385 ## [v3.5.8](https://github.com/sanger-pathogens/Roary/tree/v3.5.8) (2016-01-20)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	386 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.7...v3.5.8)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	387
c47a5f61bc9f Uploaded dereeper parents: diff changeset	388 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	389
c47a5f61bc9f Uploaded dereeper parents: diff changeset	390 - Getting Roary into Debian Med [\#219](https://github.com/sanger-pathogens/Roary/issues/219)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	391 - Add embl output file mapping location of each core gene in the core genome alignment [\#192](https://github.com/sanger-pathogens/Roary/issues/192)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	392
c47a5f61bc9f Uploaded dereeper parents: diff changeset	393 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	394
c47a5f61bc9f Uploaded dereeper parents: diff changeset	395 - Error message: Cannot find the mcxdeblast executable, please ensure its in your PATH [\#217](https://github.com/sanger-pathogens/Roary/issues/217)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	396
c47a5f61bc9f Uploaded dereeper parents: diff changeset	397 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	398
c47a5f61bc9f Uploaded dereeper parents: diff changeset	399 - Provide full accessory for building binary tree [\#227](https://github.com/sanger-pathogens/Roary/pull/227) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	400 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	401 - Debian nitpicks [\#220](https://github.com/sanger-pathogens/Roary/pull/220) ([satta](https://github.com/satta))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	402 - Core alignment header file [\#218](https://github.com/sanger-pathogens/Roary/pull/218) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	403
c47a5f61bc9f Uploaded dereeper parents: diff changeset	404 ## [v3.5.7](https://github.com/sanger-pathogens/Roary/tree/v3.5.7) (2015-12-17)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	405 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.6...v3.5.7)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	406
c47a5f61bc9f Uploaded dereeper parents: diff changeset	407 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	408
c47a5f61bc9f Uploaded dereeper parents: diff changeset	409 - Roary not checking tools needed to run [\#214](https://github.com/sanger-pathogens/Roary/issues/214)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	410
c47a5f61bc9f Uploaded dereeper parents: diff changeset	411 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	412
c47a5f61bc9f Uploaded dereeper parents: diff changeset	413 - Core gene count [\#213](https://github.com/sanger-pathogens/Roary/pull/213) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	414
c47a5f61bc9f Uploaded dereeper parents: diff changeset	415 ## [v3.5.6](https://github.com/sanger-pathogens/Roary/tree/v3.5.6) (2015-12-01)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	416 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.5...v3.5.6)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	417
c47a5f61bc9f Uploaded dereeper parents: diff changeset	418 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	419
c47a5f61bc9f Uploaded dereeper parents: diff changeset	420 - Non-issue, FYI regarding my 'roary2svg.pl' script [\#195](https://github.com/sanger-pathogens/Roary/issues/195)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	421
c47a5f61bc9f Uploaded dereeper parents: diff changeset	422 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	423
c47a5f61bc9f Uploaded dereeper parents: diff changeset	424 - add roary2svg script [\#212](https://github.com/sanger-pathogens/Roary/pull/212) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	425
c47a5f61bc9f Uploaded dereeper parents: diff changeset	426 ## [v3.5.5](https://github.com/sanger-pathogens/Roary/tree/v3.5.5) (2015-11-26)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	427 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.4...v3.5.5)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	428
c47a5f61bc9f Uploaded dereeper parents: diff changeset	429 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	430
c47a5f61bc9f Uploaded dereeper parents: diff changeset	431 - CD-hit threads limit [\#211](https://github.com/sanger-pathogens/Roary/pull/211) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	432
c47a5f61bc9f Uploaded dereeper parents: diff changeset	433 ## [v3.5.4](https://github.com/sanger-pathogens/Roary/tree/v3.5.4) (2015-11-26)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	434 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.3...v3.5.4)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	435
c47a5f61bc9f Uploaded dereeper parents: diff changeset	436 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	437
c47a5f61bc9f Uploaded dereeper parents: diff changeset	438 - Use of uninitialized value in require at $eval ..$ line 1. [\#204](https://github.com/sanger-pathogens/Roary/issues/204)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	439 - \[bug\] Newick files in 3.5.1 have branch lengths of 0.0 [\#202](https://github.com/sanger-pathogens/Roary/issues/202)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	440
c47a5f61bc9f Uploaded dereeper parents: diff changeset	441 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	442
c47a5f61bc9f Uploaded dereeper parents: diff changeset	443 - Accessory binary fasta contains all C's fix [\#210](https://github.com/sanger-pathogens/Roary/pull/210) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	444
c47a5f61bc9f Uploaded dereeper parents: diff changeset	445 ## [v3.5.3](https://github.com/sanger-pathogens/Roary/tree/v3.5.3) (2015-11-26)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	446 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.2...v3.5.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	447
c47a5f61bc9f Uploaded dereeper parents: diff changeset	448 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	449
c47a5f61bc9f Uploaded dereeper parents: diff changeset	450 - Enhancement: roary -a to continue on if other parameters as well [\#207](https://github.com/sanger-pathogens/Roary/issues/207)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	451 - Make summary\_statistics a TAB/TSV file? [\#193](https://github.com/sanger-pathogens/Roary/issues/193)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	452
c47a5f61bc9f Uploaded dereeper parents: diff changeset	453 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	454
c47a5f61bc9f Uploaded dereeper parents: diff changeset	455 - roary --version should return 0 not 255 exit code [\#206](https://github.com/sanger-pathogens/Roary/issues/206)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	456 - Is the roary -a check complete? [\#205](https://github.com/sanger-pathogens/Roary/issues/205)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	457
c47a5f61bc9f Uploaded dereeper parents: diff changeset	458 ## [v3.5.2](https://github.com/sanger-pathogens/Roary/tree/v3.5.2) (2015-11-25)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	459 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.1...v3.5.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	460
c47a5f61bc9f Uploaded dereeper parents: diff changeset	461 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	462
c47a5f61bc9f Uploaded dereeper parents: diff changeset	463 - Use of uninitialized value in File::Slurper and Encode.pm [\#196](https://github.com/sanger-pathogens/Roary/issues/196)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	464
c47a5f61bc9f Uploaded dereeper parents: diff changeset	465 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	466
c47a5f61bc9f Uploaded dereeper parents: diff changeset	467 - Improved dependancy checking [\#209](https://github.com/sanger-pathogens/Roary/pull/209) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	468 - Lsf update gene alignments [\#201](https://github.com/sanger-pathogens/Roary/pull/201) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	469
c47a5f61bc9f Uploaded dereeper parents: diff changeset	470 ## [v3.5.1](https://github.com/sanger-pathogens/Roary/tree/v3.5.1) (2015-11-12)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	471 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.5.0...v3.5.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	472
c47a5f61bc9f Uploaded dereeper parents: diff changeset	473 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	474
c47a5f61bc9f Uploaded dereeper parents: diff changeset	475 - Accessory genes newick file contains full path of infividual files [\#200](https://github.com/sanger-pathogens/Roary/issues/200)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	476 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	477
c47a5f61bc9f Uploaded dereeper parents: diff changeset	478 ## [v3.5.0](https://github.com/sanger-pathogens/Roary/tree/v3.5.0) (2015-11-12)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	479 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.3...v3.5.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	480
c47a5f61bc9f Uploaded dereeper parents: diff changeset	481 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	482
c47a5f61bc9f Uploaded dereeper parents: diff changeset	483 - remove path from accessory tree [\#198](https://github.com/sanger-pathogens/Roary/pull/198) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	484
c47a5f61bc9f Uploaded dereeper parents: diff changeset	485 ## [v3.4.3](https://github.com/sanger-pathogens/Roary/tree/v3.4.3) (2015-11-11)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	486 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.2...v3.4.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	487
c47a5f61bc9f Uploaded dereeper parents: diff changeset	488 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	489
c47a5f61bc9f Uploaded dereeper parents: diff changeset	490 - consensus group name for pan reference [\#190](https://github.com/sanger-pathogens/Roary/pull/190) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	491
c47a5f61bc9f Uploaded dereeper parents: diff changeset	492 ## [v3.4.2](https://github.com/sanger-pathogens/Roary/tree/v3.4.2) (2015-10-12)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	493 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.1...v3.4.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	494
c47a5f61bc9f Uploaded dereeper parents: diff changeset	495 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	496
c47a5f61bc9f Uploaded dereeper parents: diff changeset	497 - Gene presence and absence rtab [\#189](https://github.com/sanger-pathogens/Roary/pull/189) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	498
c47a5f61bc9f Uploaded dereeper parents: diff changeset	499 ## [v3.4.1](https://github.com/sanger-pathogens/Roary/tree/v3.4.1) (2015-10-08)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	500 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.4.0...v3.4.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	501
c47a5f61bc9f Uploaded dereeper parents: diff changeset	502 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	503
c47a5f61bc9f Uploaded dereeper parents: diff changeset	504 - Need protein lengths in the final spreadsheet [\#116](https://github.com/sanger-pathogens/Roary/issues/116)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	505
c47a5f61bc9f Uploaded dereeper parents: diff changeset	506 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	507
c47a5f61bc9f Uploaded dereeper parents: diff changeset	508 - Bio-RetrieveAssemblies-1.0.1 fails to install [\#151](https://github.com/sanger-pathogens/Roary/issues/151)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	509
c47a5f61bc9f Uploaded dereeper parents: diff changeset	510 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	511
c47a5f61bc9f Uploaded dereeper parents: diff changeset	512 - \* Proposed fix for CPANTS error. [\#187](https://github.com/sanger-pathogens/Roary/pull/187) ([manwar](https://github.com/manwar))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	513
c47a5f61bc9f Uploaded dereeper parents: diff changeset	514 ## [v3.4.0](https://github.com/sanger-pathogens/Roary/tree/v3.4.0) (2015-10-07)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	515 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.4...v3.4.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	516
c47a5f61bc9f Uploaded dereeper parents: diff changeset	517 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	518
c47a5f61bc9f Uploaded dereeper parents: diff changeset	519 - Extra columns in spreadsheet with gene lengths [\#186](https://github.com/sanger-pathogens/Roary/pull/186) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	520
c47a5f61bc9f Uploaded dereeper parents: diff changeset	521 ## [v3.3.4](https://github.com/sanger-pathogens/Roary/tree/v3.3.4) (2015-10-07)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	522 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.3...v3.3.4)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	523
c47a5f61bc9f Uploaded dereeper parents: diff changeset	524 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	525
c47a5f61bc9f Uploaded dereeper parents: diff changeset	526 - EXCEPTION: Bio::Root::Exception could not read ...faa.intermediate.extracted.fa [\#175](https://github.com/sanger-pathogens/Roary/issues/175)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	527
c47a5f61bc9f Uploaded dereeper parents: diff changeset	528 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	529
c47a5f61bc9f Uploaded dereeper parents: diff changeset	530 - increase dependancy RAM [\#185](https://github.com/sanger-pathogens/Roary/pull/185) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	531 - Use lsf for gene alignment [\#184](https://github.com/sanger-pathogens/Roary/pull/184) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	532
c47a5f61bc9f Uploaded dereeper parents: diff changeset	533 ## [v3.3.3](https://github.com/sanger-pathogens/Roary/tree/v3.3.3) (2015-09-29)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	534 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.2...v3.3.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	535
c47a5f61bc9f Uploaded dereeper parents: diff changeset	536 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	537
c47a5f61bc9f Uploaded dereeper parents: diff changeset	538 - dont align if sequences same length and nearly the same [\#183](https://github.com/sanger-pathogens/Roary/pull/183) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	539
c47a5f61bc9f Uploaded dereeper parents: diff changeset	540 ## [v3.3.2](https://github.com/sanger-pathogens/Roary/tree/v3.3.2) (2015-09-28)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	541 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.1...v3.3.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	542
c47a5f61bc9f Uploaded dereeper parents: diff changeset	543 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	544
c47a5f61bc9f Uploaded dereeper parents: diff changeset	545 - Use of temporary folders and files [\#177](https://github.com/sanger-pathogens/Roary/issues/177)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	546
c47a5f61bc9f Uploaded dereeper parents: diff changeset	547 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	548
c47a5f61bc9f Uploaded dereeper parents: diff changeset	549 - Duplicate sequences in pan genome reference fasta [\#182](https://github.com/sanger-pathogens/Roary/pull/182) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	550
c47a5f61bc9f Uploaded dereeper parents: diff changeset	551 ## [v3.3.1](https://github.com/sanger-pathogens/Roary/tree/v3.3.1) (2015-09-25)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	552 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.3.0...v3.3.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	553
c47a5f61bc9f Uploaded dereeper parents: diff changeset	554 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	555
c47a5f61bc9f Uploaded dereeper parents: diff changeset	556 - Fix usage text [\#181](https://github.com/sanger-pathogens/Roary/pull/181) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	557
c47a5f61bc9f Uploaded dereeper parents: diff changeset	558 ## [v3.3.0](https://github.com/sanger-pathogens/Roary/tree/v3.3.0) (2015-09-24)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	559 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.9...v3.3.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	560
c47a5f61bc9f Uploaded dereeper parents: diff changeset	561 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	562
c47a5f61bc9f Uploaded dereeper parents: diff changeset	563 - Check at least 2 gff files have been passed in [\#171](https://github.com/sanger-pathogens/Roary/issues/171)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	564 - Pentuple memory for worst case sCenario [\#170](https://github.com/sanger-pathogens/Roary/issues/170)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	565 - 00\_requires\_external.t missing "mafft" ? [\#168](https://github.com/sanger-pathogens/Roary/issues/168)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	566
c47a5f61bc9f Uploaded dereeper parents: diff changeset	567 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	568
c47a5f61bc9f Uploaded dereeper parents: diff changeset	569 - Check dependancies [\#180](https://github.com/sanger-pathogens/Roary/pull/180) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	570
c47a5f61bc9f Uploaded dereeper parents: diff changeset	571 ## [v3.2.9](https://github.com/sanger-pathogens/Roary/tree/v3.2.9) (2015-09-23)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	572 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.8...v3.2.9)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	573
c47a5f61bc9f Uploaded dereeper parents: diff changeset	574 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	575
c47a5f61bc9f Uploaded dereeper parents: diff changeset	576 - Add --outdir option to avoid blatting current directory [\#176](https://github.com/sanger-pathogens/Roary/issues/176)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	577
c47a5f61bc9f Uploaded dereeper parents: diff changeset	578 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	579
c47a5f61bc9f Uploaded dereeper parents: diff changeset	580 - CPAN install failure "unknown option mafft" [\#169](https://github.com/sanger-pathogens/Roary/issues/169)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	581
c47a5f61bc9f Uploaded dereeper parents: diff changeset	582 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	583
c47a5f61bc9f Uploaded dereeper parents: diff changeset	584 - Error "Cant open file: \_uninflated\_mcl\_groups" [\#179](https://github.com/sanger-pathogens/Roary/issues/179)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	585
c47a5f61bc9f Uploaded dereeper parents: diff changeset	586 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	587
c47a5f61bc9f Uploaded dereeper parents: diff changeset	588 - Add the option to specify an output directory [\#178](https://github.com/sanger-pathogens/Roary/pull/178) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	589
c47a5f61bc9f Uploaded dereeper parents: diff changeset	590 ## [v3.2.8](https://github.com/sanger-pathogens/Roary/tree/v3.2.8) (2015-09-23)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	591 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.7...v3.2.8)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	592
c47a5f61bc9f Uploaded dereeper parents: diff changeset	593 ## [v3.2.7](https://github.com/sanger-pathogens/Roary/tree/v3.2.7) (2015-09-02)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	594 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.6...v3.2.7)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	595
c47a5f61bc9f Uploaded dereeper parents: diff changeset	596 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	597
c47a5f61bc9f Uploaded dereeper parents: diff changeset	598 - count paralogs correctly when looking for differences in datasets [\#174](https://github.com/sanger-pathogens/Roary/pull/174) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	599
c47a5f61bc9f Uploaded dereeper parents: diff changeset	600 ## [v3.2.6](https://github.com/sanger-pathogens/Roary/tree/v3.2.6) (2015-09-02)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	601 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.5...v3.2.6)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	602
c47a5f61bc9f Uploaded dereeper parents: diff changeset	603 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	604
c47a5f61bc9f Uploaded dereeper parents: diff changeset	605 - revert core tree generation [\#173](https://github.com/sanger-pathogens/Roary/pull/173) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	606
c47a5f61bc9f Uploaded dereeper parents: diff changeset	607 ## [v3.2.5](https://github.com/sanger-pathogens/Roary/tree/v3.2.5) (2015-08-17)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	608 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.4...v3.2.5)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	609
c47a5f61bc9f Uploaded dereeper parents: diff changeset	610 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	611
c47a5f61bc9f Uploaded dereeper parents: diff changeset	612 - Verbose stats [\#172](https://github.com/sanger-pathogens/Roary/pull/172) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	613 - dont set bioperl version [\#167](https://github.com/sanger-pathogens/Roary/pull/167) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	614
c47a5f61bc9f Uploaded dereeper parents: diff changeset	615 ## [v3.2.4](https://github.com/sanger-pathogens/Roary/tree/v3.2.4) (2015-07-23)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	616 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.3...v3.2.4)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	617
c47a5f61bc9f Uploaded dereeper parents: diff changeset	618 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	619
c47a5f61bc9f Uploaded dereeper parents: diff changeset	620 - update readme citation [\#165](https://github.com/sanger-pathogens/Roary/pull/165) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	621
c47a5f61bc9f Uploaded dereeper parents: diff changeset	622 ## [v3.2.3](https://github.com/sanger-pathogens/Roary/tree/v3.2.3) (2015-07-22)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	623 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.1...v3.2.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	624
c47a5f61bc9f Uploaded dereeper parents: diff changeset	625 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	626
c47a5f61bc9f Uploaded dereeper parents: diff changeset	627 - update citation message [\#164](https://github.com/sanger-pathogens/Roary/pull/164) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	628 - Pass mafft through to alignment [\#163](https://github.com/sanger-pathogens/Roary/pull/163) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	629
c47a5f61bc9f Uploaded dereeper parents: diff changeset	630 ## [v3.2.1](https://github.com/sanger-pathogens/Roary/tree/v3.2.1) (2015-07-21)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	631 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.2.0...v3.2.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	632
c47a5f61bc9f Uploaded dereeper parents: diff changeset	633 ## [v3.2.0](https://github.com/sanger-pathogens/Roary/tree/v3.2.0) (2015-07-20)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	634 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.2...v3.2.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	635
c47a5f61bc9f Uploaded dereeper parents: diff changeset	636 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	637
c47a5f61bc9f Uploaded dereeper parents: diff changeset	638 - Use mafft [\#162](https://github.com/sanger-pathogens/Roary/pull/162) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	639 - output summary file [\#161](https://github.com/sanger-pathogens/Roary/pull/161) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	640 - Pass through dont delete flag [\#160](https://github.com/sanger-pathogens/Roary/pull/160) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	641 - Assembly statistics [\#159](https://github.com/sanger-pathogens/Roary/pull/159) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	642
c47a5f61bc9f Uploaded dereeper parents: diff changeset	643 ## [v3.1.2](https://github.com/sanger-pathogens/Roary/tree/v3.1.2) (2015-07-13)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	644 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/3.1.2...v3.1.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	645
c47a5f61bc9f Uploaded dereeper parents: diff changeset	646 ## [3.1.2](https://github.com/sanger-pathogens/Roary/tree/3.1.2) (2015-07-13)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	647 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.1...3.1.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	648
c47a5f61bc9f Uploaded dereeper parents: diff changeset	649 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	650
c47a5f61bc9f Uploaded dereeper parents: diff changeset	651 - prank seg fault [\#157](https://github.com/sanger-pathogens/Roary/issues/157)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	652
c47a5f61bc9f Uploaded dereeper parents: diff changeset	653 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	654
c47a5f61bc9f Uploaded dereeper parents: diff changeset	655 - Core gene missing files [\#158](https://github.com/sanger-pathogens/Roary/pull/158) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	656
c47a5f61bc9f Uploaded dereeper parents: diff changeset	657 ## [v3.1.1](https://github.com/sanger-pathogens/Roary/tree/v3.1.1) (2015-06-26)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	658 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.1.0...v3.1.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	659
c47a5f61bc9f Uploaded dereeper parents: diff changeset	660 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	661
c47a5f61bc9f Uploaded dereeper parents: diff changeset	662 - sadaf [\#154](https://github.com/sanger-pathogens/Roary/issues/154)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	663
c47a5f61bc9f Uploaded dereeper parents: diff changeset	664 ## [v3.1.0](https://github.com/sanger-pathogens/Roary/tree/v3.1.0) (2015-06-22)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	665 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.3...v3.1.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	666
c47a5f61bc9f Uploaded dereeper parents: diff changeset	667 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	668
c47a5f61bc9f Uploaded dereeper parents: diff changeset	669 - Accessory binary tree [\#155](https://github.com/sanger-pathogens/Roary/pull/155) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	670
c47a5f61bc9f Uploaded dereeper parents: diff changeset	671 ## [v3.0.3](https://github.com/sanger-pathogens/Roary/tree/v3.0.3) (2015-06-15)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	672 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.2...v3.0.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	673
c47a5f61bc9f Uploaded dereeper parents: diff changeset	674 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	675
c47a5f61bc9f Uploaded dereeper parents: diff changeset	676 - Annotation missing in set\_difference\_unique\_set\_one/two\_statistics.csv files [\#137](https://github.com/sanger-pathogens/Roary/issues/137)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	677
c47a5f61bc9f Uploaded dereeper parents: diff changeset	678 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	679
c47a5f61bc9f Uploaded dereeper parents: diff changeset	680 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	681 - Only align core files [\#150](https://github.com/sanger-pathogens/Roary/pull/150) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	682
c47a5f61bc9f Uploaded dereeper parents: diff changeset	683 ## [v3.0.2](https://github.com/sanger-pathogens/Roary/tree/v3.0.2) (2015-06-12)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	684 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.1...v3.0.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	685
c47a5f61bc9f Uploaded dereeper parents: diff changeset	686 Implemented enhancements:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	687
c47a5f61bc9f Uploaded dereeper parents: diff changeset	688 - Print out the version number [\#119](https://github.com/sanger-pathogens/Roary/issues/119)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	689
c47a5f61bc9f Uploaded dereeper parents: diff changeset	690 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	691
c47a5f61bc9f Uploaded dereeper parents: diff changeset	692 - Mafft and exonerate dependancies [\#149](https://github.com/sanger-pathogens/Roary/pull/149) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	693 - Add a version parameter and add in marcos plots code [\#148](https://github.com/sanger-pathogens/Roary/pull/148) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	694
c47a5f61bc9f Uploaded dereeper parents: diff changeset	695 ## [v3.0.1](https://github.com/sanger-pathogens/Roary/tree/v3.0.1) (2015-06-12)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	696 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v3.0.0...v3.0.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	697
c47a5f61bc9f Uploaded dereeper parents: diff changeset	698 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	699
c47a5f61bc9f Uploaded dereeper parents: diff changeset	700 - Use of -e switch gives multifasta file with N's only [\#132](https://github.com/sanger-pathogens/Roary/issues/132)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	701
c47a5f61bc9f Uploaded dereeper parents: diff changeset	702 ## [v3.0.0](https://github.com/sanger-pathogens/Roary/tree/v3.0.0) (2015-06-11)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	703 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.4...v3.0.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	704
c47a5f61bc9f Uploaded dereeper parents: diff changeset	705 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	706
c47a5f61bc9f Uploaded dereeper parents: diff changeset	707 - Use prank for core genome alignments [\#147](https://github.com/sanger-pathogens/Roary/pull/147) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	708 - Accessory graph [\#146](https://github.com/sanger-pathogens/Roary/pull/146) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	709
c47a5f61bc9f Uploaded dereeper parents: diff changeset	710 ## [v2.3.4](https://github.com/sanger-pathogens/Roary/tree/v2.3.4) (2015-06-10)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	711 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.3...v2.3.4)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	712
c47a5f61bc9f Uploaded dereeper parents: diff changeset	713 ## [v2.3.3](https://github.com/sanger-pathogens/Roary/tree/v2.3.3) (2015-06-08)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	714 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.2...v2.3.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	715
c47a5f61bc9f Uploaded dereeper parents: diff changeset	716 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	717
c47a5f61bc9f Uploaded dereeper parents: diff changeset	718 - Simplify perl dependency installation [\#145](https://github.com/sanger-pathogens/Roary/pull/145) ([bewt85](https://github.com/bewt85))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	719 - Pan genome reference [\#144](https://github.com/sanger-pathogens/Roary/pull/144) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	720 - Fix input files with duplicate IDs [\#143](https://github.com/sanger-pathogens/Roary/pull/143) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	721 - Test against different versions of GNU Parallel [\#142](https://github.com/sanger-pathogens/Roary/pull/142) ([bewt85](https://github.com/bewt85))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	722
c47a5f61bc9f Uploaded dereeper parents: diff changeset	723 ## [v2.3.2](https://github.com/sanger-pathogens/Roary/tree/v2.3.2) (2015-06-08)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	724 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.1...v2.3.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	725
c47a5f61bc9f Uploaded dereeper parents: diff changeset	726 Fixed bugs:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	727
c47a5f61bc9f Uploaded dereeper parents: diff changeset	728 - GFF files derived from Prokka genbank raise errors [\#130](https://github.com/sanger-pathogens/Roary/issues/130)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	729 - MSG: Got a sequence without letters. Could not guess alphabet [\#127](https://github.com/sanger-pathogens/Roary/issues/127)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	730
c47a5f61bc9f Uploaded dereeper parents: diff changeset	731 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	732
c47a5f61bc9f Uploaded dereeper parents: diff changeset	733 - TravisCI only wants the major and minor version of perl [\#141](https://github.com/sanger-pathogens/Roary/pull/141) ([bewt85](https://github.com/bewt85))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	734 - Add TravisCI support [\#140](https://github.com/sanger-pathogens/Roary/pull/140) ([bewt85](https://github.com/bewt85))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	735 - Use locus tag when ID is missing from GFF [\#139](https://github.com/sanger-pathogens/Roary/pull/139) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	736
c47a5f61bc9f Uploaded dereeper parents: diff changeset	737 ## [v2.3.1](https://github.com/sanger-pathogens/Roary/tree/v2.3.1) (2015-06-02)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	738 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.3.0...v2.3.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	739
c47a5f61bc9f Uploaded dereeper parents: diff changeset	740 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	741
c47a5f61bc9f Uploaded dereeper parents: diff changeset	742 - Extract IDs from GFF file using Bio::Perl [\#138](https://github.com/sanger-pathogens/Roary/pull/138) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	743
c47a5f61bc9f Uploaded dereeper parents: diff changeset	744 ## [v2.3.0](https://github.com/sanger-pathogens/Roary/tree/v2.3.0) (2015-06-01)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	745 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.6...v2.3.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	746
c47a5f61bc9f Uploaded dereeper parents: diff changeset	747 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	748
c47a5f61bc9f Uploaded dereeper parents: diff changeset	749 - "cpan" command reports Bio::Roary as version '$undef$' [\#134](https://github.com/sanger-pathogens/Roary/issues/134)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	750
c47a5f61bc9f Uploaded dereeper parents: diff changeset	751 ## [v2.2.6](https://github.com/sanger-pathogens/Roary/tree/v2.2.6) (2015-06-01)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	752 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.4...v2.2.6)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	753
c47a5f61bc9f Uploaded dereeper parents: diff changeset	754 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	755
c47a5f61bc9f Uploaded dereeper parents: diff changeset	756 - No tagged release for 2.2.3 [\#133](https://github.com/sanger-pathogens/Roary/issues/133)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	757 - Syntax $?$ errors on perl 5.10.1 [\#128](https://github.com/sanger-pathogens/Roary/issues/128)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	758
c47a5f61bc9f Uploaded dereeper parents: diff changeset	759 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	760
c47a5f61bc9f Uploaded dereeper parents: diff changeset	761 - include version numbers for cpan [\#136](https://github.com/sanger-pathogens/Roary/pull/136) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	762 - New version number for contributed fix for issue \#128 [\#135](https://github.com/sanger-pathogens/Roary/pull/135) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	763 - gnu parallel switch for ubuntu [\#131](https://github.com/sanger-pathogens/Roary/pull/131) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	764 - Backward compatible deferencing of hashes [\#129](https://github.com/sanger-pathogens/Roary/pull/129) ([mgalardini](https://github.com/mgalardini))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	765
c47a5f61bc9f Uploaded dereeper parents: diff changeset	766 ## [v2.2.4](https://github.com/sanger-pathogens/Roary/tree/v2.2.4) (2015-05-29)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	767 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.3...v2.2.4)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	768
c47a5f61bc9f Uploaded dereeper parents: diff changeset	769 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	770
c47a5f61bc9f Uploaded dereeper parents: diff changeset	771 - ERROR: cannot remove directory for split\_groups [\#115](https://github.com/sanger-pathogens/Roary/issues/115)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	772 - cleanup outputfiles [\#114](https://github.com/sanger-pathogens/Roary/issues/114)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	773
c47a5f61bc9f Uploaded dereeper parents: diff changeset	774 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	775
c47a5f61bc9f Uploaded dereeper parents: diff changeset	776 - Cleanup files [\#126](https://github.com/sanger-pathogens/Roary/pull/126) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	777
c47a5f61bc9f Uploaded dereeper parents: diff changeset	778 ## [v2.2.3](https://github.com/sanger-pathogens/Roary/tree/v2.2.3) (2015-05-21)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	779 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.2...v2.2.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	780
c47a5f61bc9f Uploaded dereeper parents: diff changeset	781 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	782
c47a5f61bc9f Uploaded dereeper parents: diff changeset	783 - Change QC so that it doesnt shred reads [\#117](https://github.com/sanger-pathogens/Roary/issues/117)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	784 - QC doesnt work outside sanger [\#112](https://github.com/sanger-pathogens/Roary/issues/112)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	785
c47a5f61bc9f Uploaded dereeper parents: diff changeset	786 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	787
c47a5f61bc9f Uploaded dereeper parents: diff changeset	788 - Update Kraken QC [\#125](https://github.com/sanger-pathogens/Roary/pull/125) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	789
c47a5f61bc9f Uploaded dereeper parents: diff changeset	790 ## [v2.2.2](https://github.com/sanger-pathogens/Roary/tree/v2.2.2) (2015-05-21)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	791 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.2.0...v2.2.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	792
c47a5f61bc9f Uploaded dereeper parents: diff changeset	793 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	794
c47a5f61bc9f Uploaded dereeper parents: diff changeset	795 - Hard-coded Sanger paths in some scripts [\#124](https://github.com/sanger-pathogens/Roary/issues/124)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	796 - You're missing some Perl dependancies [\#123](https://github.com/sanger-pathogens/Roary/issues/123)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	797 - Add support for GFF files from NCBI [\#120](https://github.com/sanger-pathogens/Roary/issues/120)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	798
c47a5f61bc9f Uploaded dereeper parents: diff changeset	799 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	800
c47a5f61bc9f Uploaded dereeper parents: diff changeset	801 - Fix usage text [\#122](https://github.com/sanger-pathogens/Roary/pull/122) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	802
c47a5f61bc9f Uploaded dereeper parents: diff changeset	803 ## [v2.2.0](https://github.com/sanger-pathogens/Roary/tree/v2.2.0) (2015-05-14)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	804 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.2...v2.2.0)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	805
c47a5f61bc9f Uploaded dereeper parents: diff changeset	806 Closed issues:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	807
c47a5f61bc9f Uploaded dereeper parents: diff changeset	808 - Verbose output with -v [\#113](https://github.com/sanger-pathogens/Roary/issues/113)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	809
c47a5f61bc9f Uploaded dereeper parents: diff changeset	810 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	811
c47a5f61bc9f Uploaded dereeper parents: diff changeset	812 - Accept genbank files [\#121](https://github.com/sanger-pathogens/Roary/pull/121) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	813
c47a5f61bc9f Uploaded dereeper parents: diff changeset	814 ## [v2.1.2](https://github.com/sanger-pathogens/Roary/tree/v2.1.2) (2015-05-12)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	815 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.1.1...v2.1.2)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	816
c47a5f61bc9f Uploaded dereeper parents: diff changeset	817 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	818
c47a5f61bc9f Uploaded dereeper parents: diff changeset	819 - Verbose output [\#118](https://github.com/sanger-pathogens/Roary/pull/118) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	820
c47a5f61bc9f Uploaded dereeper parents: diff changeset	821 ## [v2.1.1](https://github.com/sanger-pathogens/Roary/tree/v2.1.1) (2015-04-29)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	822 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.9...v2.1.1)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	823
c47a5f61bc9f Uploaded dereeper parents: diff changeset	824 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	825
c47a5f61bc9f Uploaded dereeper parents: diff changeset	826 - pass core definition into number of conserved genes plot [\#111](https://github.com/sanger-pathogens/Roary/pull/111) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	827 - Vary core definition [\#110](https://github.com/sanger-pathogens/Roary/pull/110) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	828 - Use block quotes in readme [\#109](https://github.com/sanger-pathogens/Roary/pull/109) ([bewt85](https://github.com/bewt85))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	829
c47a5f61bc9f Uploaded dereeper parents: diff changeset	830 ## [v2.0.9](https://github.com/sanger-pathogens/Roary/tree/v2.0.9) (2015-04-20)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	831 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.8...v2.0.9)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	832
c47a5f61bc9f Uploaded dereeper parents: diff changeset	833 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	834
c47a5f61bc9f Uploaded dereeper parents: diff changeset	835 - Allow for multiple processors to be used [\#108](https://github.com/sanger-pathogens/Roary/pull/108) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	836
c47a5f61bc9f Uploaded dereeper parents: diff changeset	837 ## [v2.0.8](https://github.com/sanger-pathogens/Roary/tree/v2.0.8) (2015-04-09)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	838 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.7...v2.0.8)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	839
c47a5f61bc9f Uploaded dereeper parents: diff changeset	840 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	841
c47a5f61bc9f Uploaded dereeper parents: diff changeset	842 - Speedup [\#107](https://github.com/sanger-pathogens/Roary/pull/107) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	843 - new version 2.0.7 [\#106](https://github.com/sanger-pathogens/Roary/pull/106) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	844
c47a5f61bc9f Uploaded dereeper parents: diff changeset	845 ## [v2.0.7](https://github.com/sanger-pathogens/Roary/tree/v2.0.7) (2015-03-28)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	846 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.5...v2.0.7)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	847
c47a5f61bc9f Uploaded dereeper parents: diff changeset	848 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	849
c47a5f61bc9f Uploaded dereeper parents: diff changeset	850 - old splits [\#105](https://github.com/sanger-pathogens/Roary/pull/105) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	851 - Speedup split [\#104](https://github.com/sanger-pathogens/Roary/pull/104) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	852
c47a5f61bc9f Uploaded dereeper parents: diff changeset	853 ## [v2.0.5](https://github.com/sanger-pathogens/Roary/tree/v2.0.5) (2015-03-26)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	854 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.4...v2.0.5)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	855
c47a5f61bc9f Uploaded dereeper parents: diff changeset	856 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	857
c47a5f61bc9f Uploaded dereeper parents: diff changeset	858 - Stop deep recursion [\#103](https://github.com/sanger-pathogens/Roary/pull/103) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	859 - check programs installed [\#102](https://github.com/sanger-pathogens/Roary/pull/102) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	860
c47a5f61bc9f Uploaded dereeper parents: diff changeset	861 ## [2.0.4](https://github.com/sanger-pathogens/Roary/tree/2.0.4) (2015-03-23)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	862 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/2.0.3...2.0.4)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	863
c47a5f61bc9f Uploaded dereeper parents: diff changeset	864 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	865
c47a5f61bc9f Uploaded dereeper parents: diff changeset	866 - File slurp tiny [\#101](https://github.com/sanger-pathogens/Roary/pull/101) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	867 - version 2.0.3 [\#100](https://github.com/sanger-pathogens/Roary/pull/100) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	868
c47a5f61bc9f Uploaded dereeper parents: diff changeset	869 ## [2.0.3](https://github.com/sanger-pathogens/Roary/tree/2.0.3) (2015-03-17)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	870 [Full Changelog](https://github.com/sanger-pathogens/Roary/compare/v2.0.0...2.0.3)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	871
c47a5f61bc9f Uploaded dereeper parents: diff changeset	872 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	873
c47a5f61bc9f Uploaded dereeper parents: diff changeset	874 - Remove LSF support [\#99](https://github.com/sanger-pathogens/Roary/pull/99) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	875 - Dont set LSF as the default runner [\#98](https://github.com/sanger-pathogens/Roary/pull/98) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	876 - Rename directories to Roary [\#97](https://github.com/sanger-pathogens/Roary/pull/97) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	877
c47a5f61bc9f Uploaded dereeper parents: diff changeset	878 ## [v2.0.0](https://github.com/sanger-pathogens/Roary/tree/v2.0.0) (2015-03-16)
c47a5f61bc9f Uploaded dereeper parents: diff changeset	879 Merged pull requests:
c47a5f61bc9f Uploaded dereeper parents: diff changeset	880
c47a5f61bc9f Uploaded dereeper parents: diff changeset	881 - Ship binaries [\#96](https://github.com/sanger-pathogens/Roary/pull/96) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	882 - Pad merged multifastas when data is missing [\#95](https://github.com/sanger-pathogens/Roary/pull/95) ([carlacummins](https://github.com/carlacummins))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	883 - Subsample reads [\#94](https://github.com/sanger-pathogens/Roary/pull/94) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	884 - Merge Carlas CGN [\#93](https://github.com/sanger-pathogens/Roary/pull/93) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	885 - rename spreadsheet [\#92](https://github.com/sanger-pathogens/Roary/pull/92) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	886 - Refactor out fasta grep [\#91](https://github.com/sanger-pathogens/Roary/pull/91) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	887 - remove fasta\_grep [\#90](https://github.com/sanger-pathogens/Roary/pull/90) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	888 - Add gnu parallel support [\#89](https://github.com/sanger-pathogens/Roary/pull/89) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	889 - Updated create\_pan\_genome help text to include -qc option [\#88](https://github.com/sanger-pathogens/Roary/pull/88) ([carlacummins](https://github.com/carlacummins))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	890 - QC report option added [\#87](https://github.com/sanger-pathogens/Roary/pull/87) ([carlacummins](https://github.com/carlacummins))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	891 - increase blastp min memory to 3gb from 100 [\#86](https://github.com/sanger-pathogens/Roary/pull/86) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	892 - Remove fastatranslate dependancy [\#85](https://github.com/sanger-pathogens/Roary/pull/85) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	893 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	894 - Bug fix [\#83](https://github.com/sanger-pathogens/Roary/pull/83) ([carlacummins](https://github.com/carlacummins))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	895 - Added verbose stats option [\#82](https://github.com/sanger-pathogens/Roary/pull/82) ([carlacummins](https://github.com/carlacummins))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	896 - Group limit changed to 50,000 [\#81](https://github.com/sanger-pathogens/Roary/pull/81) ([carlacummins](https://github.com/carlacummins))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	897 - Multifastas not created when group limit $default 8000$ exceeded [\#80](https://github.com/sanger-pathogens/Roary/pull/80) ([carlacummins](https://github.com/carlacummins))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	898 - allow for translation table to be passed in [\#79](https://github.com/sanger-pathogens/Roary/pull/79) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	899 - increase memory [\#78](https://github.com/sanger-pathogens/Roary/pull/78) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	900 - Allow user specify sorting when reordering spreadsheet against a tree [\#77](https://github.com/sanger-pathogens/Roary/pull/77) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	901 - Bug fixing [\#76](https://github.com/sanger-pathogens/Roary/pull/76) ([carlacummins](https://github.com/carlacummins))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	902 - Added AUTHORS file [\#75](https://github.com/sanger-pathogens/Roary/pull/75) ([aslett1](https://github.com/aslett1))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	903 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	904 - use long queue for more than 200 samples [\#73](https://github.com/sanger-pathogens/Roary/pull/73) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	905 - core alignment gets run with lsf [\#72](https://github.com/sanger-pathogens/Roary/pull/72) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	906 - Job runner ids lsf [\#71](https://github.com/sanger-pathogens/Roary/pull/71) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	907 - Core alignment missing file [\#70](https://github.com/sanger-pathogens/Roary/pull/70) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	908 - Core alignment missing file [\#69](https://github.com/sanger-pathogens/Roary/pull/69) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	909 - update error reporting [\#68](https://github.com/sanger-pathogens/Roary/pull/68) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	910 - Create core alignment from spreadsheet and multifasta files [\#67](https://github.com/sanger-pathogens/Roary/pull/67) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	911 - make script executable [\#66](https://github.com/sanger-pathogens/Roary/pull/66) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	912 - script to merge multifasta files together [\#65](https://github.com/sanger-pathogens/Roary/pull/65) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	913 - rename output gene multfastas and pass all sequences through [\#64](https://github.com/sanger-pathogens/Roary/pull/64) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	914 - Align genes at protein level and back translate to nucleotides [\#63](https://github.com/sanger-pathogens/Roary/pull/63) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	915 - Depth first search for reordering spreadsheet [\#62](https://github.com/sanger-pathogens/Roary/pull/62) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	916 - make the iterative cdhit script useful for standalone use [\#61](https://github.com/sanger-pathogens/Roary/pull/61) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	917 - query\_pan\_genome\_update\_text [\#60](https://github.com/sanger-pathogens/Roary/pull/60) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	918 - fix failing tests [\#59](https://github.com/sanger-pathogens/Roary/pull/59) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	919 - Create plot for % blast identity [\#58](https://github.com/sanger-pathogens/Roary/pull/58) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	920 - add a flag to keep intermediate files [\#57](https://github.com/sanger-pathogens/Roary/pull/57) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	921 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	922 - print fragment blocks [\#55](https://github.com/sanger-pathogens/Roary/pull/55) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	923 - Fix ordering of accessory [\#54](https://github.com/sanger-pathogens/Roary/pull/54) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	924 - fix r plots [\#53](https://github.com/sanger-pathogens/Roary/pull/53) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	925 - Overlapping proteins [\#52](https://github.com/sanger-pathogens/Roary/pull/52) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	926 - Gene order [\#51](https://github.com/sanger-pathogens/Roary/pull/51) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	927 - pass job runner to iterative cdhit [\#50](https://github.com/sanger-pathogens/Roary/pull/50) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	928 - iterative cdhit in a job [\#49](https://github.com/sanger-pathogens/Roary/pull/49) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	929 - Fix tests [\#48](https://github.com/sanger-pathogens/Roary/pull/48) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	930 - Prefilter optimisation [\#47](https://github.com/sanger-pathogens/Roary/pull/47) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	931 - dont split groups [\#46](https://github.com/sanger-pathogens/Roary/pull/46) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	932 - rename create plots R script [\#45](https://github.com/sanger-pathogens/Roary/pull/45) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	933 - cdhit should output full description of sequence name [\#44](https://github.com/sanger-pathogens/Roary/pull/44) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	934 - Gene count plot [\#43](https://github.com/sanger-pathogens/Roary/pull/43) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	935 - align gene multifasta files using muscle [\#42](https://github.com/sanger-pathogens/Roary/pull/42) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	936 - Reorder spreadsheet [\#41](https://github.com/sanger-pathogens/Roary/pull/41) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	937 - Reorder spreadsheet [\#40](https://github.com/sanger-pathogens/Roary/pull/40) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	938 - Speedup post analysis [\#39](https://github.com/sanger-pathogens/Roary/pull/39) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	939 - Presence and absence of genes [\#38](https://github.com/sanger-pathogens/Roary/pull/38) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	940 - split big groups based on annotation [\#37](https://github.com/sanger-pathogens/Roary/pull/37) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	941 - make multifasta files easier to sort [\#36](https://github.com/sanger-pathogens/Roary/pull/36) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	942 - dont wait in lfs scheduler [\#35](https://github.com/sanger-pathogens/Roary/pull/35) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	943 - run post analysis as a job [\#34](https://github.com/sanger-pathogens/Roary/pull/34) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	944 - annotate the names of the groups files [\#33](https://github.com/sanger-pathogens/Roary/pull/33) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	945 - Output all sequences making up pan genome in multifasta files [\#32](https://github.com/sanger-pathogens/Roary/pull/32) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	946 - Run external applications through lsf [\#31](https://github.com/sanger-pathogens/Roary/pull/31) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	947 - remove done dependancy job [\#30](https://github.com/sanger-pathogens/Roary/pull/30) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	948 - blocking job [\#29](https://github.com/sanger-pathogens/Roary/pull/29) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	949 - Filter unknowns in LSF jobs [\#28](https://github.com/sanger-pathogens/Roary/pull/28) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	950 - Pass job runner through to extract gffs [\#27](https://github.com/sanger-pathogens/Roary/pull/27) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	951 - Change case of GFF commandline class [\#26](https://github.com/sanger-pathogens/Roary/pull/26) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	952 - use LSF to do the inital parsing of input files [\#25](https://github.com/sanger-pathogens/Roary/pull/25) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	953 - renamed LICENSE [\#24](https://github.com/sanger-pathogens/Roary/pull/24) ([CraigPorter](https://github.com/CraigPorter))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	954 - GPL [\#23](https://github.com/sanger-pathogens/Roary/pull/23) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	955 - lsf memory in mb [\#22](https://github.com/sanger-pathogens/Roary/pull/22) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	956 - low complexity filtering [\#21](https://github.com/sanger-pathogens/Roary/pull/21) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	957 - inflate clusters where the representative gene is not the first [\#20](https://github.com/sanger-pathogens/Roary/pull/20) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	958 - report more sequences from blastp [\#19](https://github.com/sanger-pathogens/Roary/pull/19) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	959 - update tests for different input processing [\#18](https://github.com/sanger-pathogens/Roary/pull/18) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	960 - speedup extracting proteins from gff [\#17](https://github.com/sanger-pathogens/Roary/pull/17) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	961 - sort spreadsheet by number of isolates [\#16](https://github.com/sanger-pathogens/Roary/pull/16) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	962 - create spreadsheets of differences between sets [\#15](https://github.com/sanger-pathogens/Roary/pull/15) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	963 - Output statistics on groups [\#14](https://github.com/sanger-pathogens/Roary/pull/14) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	964 - Find the difference between isolates [\#13](https://github.com/sanger-pathogens/Roary/pull/13) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	965 - check if group is null [\#12](https://github.com/sanger-pathogens/Roary/pull/12) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	966 - catch undef [\#11](https://github.com/sanger-pathogens/Roary/pull/11) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	967 - tests for create pan genome script [\#10](https://github.com/sanger-pathogens/Roary/pull/10) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	968 - label fasta sequences with annotation ID [\#9](https://github.com/sanger-pathogens/Roary/pull/9) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	969 - 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))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	970 - transfer annotation [\#7](https://github.com/sanger-pathogens/Roary/pull/7) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	971 - speedup searching fastas [\#6](https://github.com/sanger-pathogens/Roary/pull/6) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	972 - typo in memory estimation [\#5](https://github.com/sanger-pathogens/Roary/pull/5) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	973 - run mcl and inflate results [\#4](https://github.com/sanger-pathogens/Roary/pull/4) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	974 - vary memory usage according to input file size [\#3](https://github.com/sanger-pathogens/Roary/pull/3) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	975 - working on real data [\#2](https://github.com/sanger-pathogens/Roary/pull/2) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	976 - Initial functionality [\#1](https://github.com/sanger-pathogens/Roary/pull/1) ([andrewjpage](https://github.com/andrewjpage))
c47a5f61bc9f Uploaded dereeper parents: diff changeset	977

Mercurial > repos > dereeper > roary_plots

annotate Roary/CHANGELOG.md @ 2:3f98630a0c20 draft