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