v3.3 (2022-10-6)
- Enable time calibration of final tree
- Use separate models for tree construction and SNP reconstruction
- Enable use of iqtree in fast mode
- Allow model testing to identify the best-fitting model for tree construction
- Fix processing of custom phylogenetic models
v3.2.1 (2022-5-24)
- Fix problem with sequence reconstruction
- Improve detection of small recombinations by modifying window sizes
- Enable resumption of stalled analyses
- Clean C code
- Fixes to scripts
- Add CI tests and update expected results
v3.1.6 (2022-1-20)
- Fix problem with sequence reconstruction
- Add test for consistency of reconstructions
v3.1.5 (2022-1-19)
- Reduce memory consumption of some C code
- Extract unique base patterns in C code
- Adapt python code to take new inputs
- Update documentation and website
v3.1.4 (2021-10-22)
- Reimplement JAR with numpy and numba
- Switch to spawn over fork for Linux multiprocessing
- Fixes bootstraps with Fasttree (#312)
- Fixes parallelisation of RAxML-NG
v3.1.3 (2021-10-22)
- Output SH tests on final tree (#314)
v3.1.2 (2021-10-12)
- Install scripts correctly
- Correct documentation
v3.1.1 (2021-10-12)
- Avoid using a single starting tree for RAxML-NG
v3.1.0 (2021-10-08)
- Adds scripts for generating inputs and processing outputs
- More thorough checking of tree topology when passing information between methods
- More detailed error handling for incorrect input alignments
v3.0.0 (2021-01-27)
Closed issues:
- Question: gubbins input? #215
Merged pull requests:
- Upgrade to version 3.0 #291 (nickjcroucher)
- remove email address #287 (puethe)
- Remove email/phone number in contact us section #281 (garethpeat)
v2.4.1 (2020-01-20)
Merged pull requests:
v2.4.0-docker2 (2020-01-13)
Closed issues:
- Specify OutPut Path or Tmp #263
Merged pull requests:
v2.4.0 (2020-01-03)
Merged pull requests:
v2.3.5 (2019-11-11)
Implemented enhancements:
- Retaining recombinant free non-polymorphic sites #208
Fixed bugs:
Closed issues:
- Gubbins not generating final_tree.tre #253
- Can gubbins take the fasta file produced by snp-sites as inputs? #250
- rho/theta--> total recombination events? #247
- Gubbins output: internal_5 / internal_6 node? #246
- recombination_predictions.gff regions are overlapping and duplicated ? #240
- Gubbins crashed, please ensure you have enough free memory #239
- GFF file output columns #234
- what does "Bases in Recombinations" in the stats file refer to? #232
- Make the FTP urls actual hyperlinks #229
- Failing test on 2.1.0 #177
Merged pull requests:
- update changelog #261 (puethe)
- Rename exec in docker #260 (puethe)
- Mark as unmaintained #259 (puethe)
- 627258 codecov #244 (ssjunnebo)
- Add changelog #242 (ssjunnebo)
- Rt574328 readme #241 (ssjunnebo)
- Remove INSTALL file #238 (ssjunnebo)
- 574328 edit readme #237 (ssjunnebo)
- update changelog #228 (puethe)
v2.3.4 (2018-07-30)
Merged pull requests:
v2.3.3 (2018-07-26)
Closed issues:
- ' INSTALL' doesn't link to INSTALL.md #222
Merged pull requests:
- Dockerfile independent from debian package #226 (puethe)
- universal link #224 (puethe)
- link to install.md #223 (puethe)
v2.3.2 (2018-06-15)
Implemented enhancements:
- Direct output to a directory #209
Fixed bugs:
- Warning while parsing tree: non-numeric label N38 for internal node #154
Closed issues:
- Is there minimum sample size to use gubbins? #213
- gubbins_drawer graph #212
- Running example files #211
- TypeError: reroot_at_midpoint() got an unexpected keyword argument 'update_splits' #205
- x #204
- Input format is not clear #185
- Inconsistencies in branch stats file #181
- error while loading shared libraries: libgubbins.so.0 #156
Merged pull requests:
- Replaced the script gubbins_drawer.py with an empty script displaying… #221 (puethe)
- Link check to lsubunit #220 (puethe)
- corrected typo: 'fastree' -> 'fasttree' #219 (puethe)
- update instructions for Docker #217 (ssjunnebo)
- added choices to
--tree\_builderand other args #207 (schultzm) - ignore ltmain.sh for language statistics #206 (ssjunnebo)
- update manual #203 (andrewjpage)
v2.3.1 (2017-09-22)
Fixed bugs:
- gubbins_drawer.py help improvement #183
Merged pull requests:
- Internal nodes #202 (andrewjpage)
v2.3.0 (2017-09-21)
Fixed bugs:
- Some options have default listed twice in --help #199
Merged pull requests:
- Gubbins drawer help text #201 (andrewjpage)
v2.2.3 (2017-09-15)
Fixed bugs:
- Error running gubbins_drawer.py with v. 2.2.0 #184
Closed issues:
- Support raxml-AVX2 if available #196
- brew install gubbins errors - no formula for pillow #194
- gubbins would not run #187
Merged pull requests:
- Fix default extended help text. #200 (andrewjpage)
- allow for AVX2 #197 (andrewjpage)
v2.2.2 (2017-09-04)
Closed issues:
- Forgot to make a 2.2.1 release? #195
v2.2.1 (2017-08-02)
Closed issues:
- Gubbins - Ns in output alignment #192
- from gubbins import common ImportError: cannot import name common #191
- Losing taxa? #189
Merged pull requests:
- updated manual #193 (ssjunnebo)
- Manual in docx format #188 (ssjunnebo)
- Fixed biopython sub_features bug #186 (ssjunnebo)
v1.4.10 (2016-10-31)
Closed issues:
- removing identical isolates #179
v2.2.0 (2016-10-31)
Closed issues:
- Linuxbrew installs 1.4.7 still #176
- Can't find RAxML in path #174
- Source install doesn't install python wrappers #173
Merged pull requests:
- dont filter out identical sequences by default #180 (andrewjpage)
v2.1.0 (2016-07-22)
Fixed bugs:
- slow fastml #167
Merged pull requests:
- Use GTRCAT by default with RAxML #175 (andrewjpage)
v2.0.0 (2016-07-15)
Closed issues:
- .embl output file not opening in Artemis #165
Merged pull requests:
- Raxml reconstruction #172 (andrewjpage)
- Raxml reconstruction #171 (andrewjpage)
v1.4.9 (2016-04-15)
Merged pull requests:
- Duplicate sequences #166 (andrewjpage)
v1.4.8 (2016-04-13)
Closed issues:
- numpy issues #159
Merged pull requests:
v1.4.7 (2016-02-29)
Merged pull requests:
- midpoint rerooting by default #163 (andrewjpage)
- Fix allocation from stack bug. #161 (jeromekelleher)
v1.4.6 (2016-02-29)
v1.4.5 (2016-01-13)
v.1.4.5 (2016-01-13)
Merged pull requests:
- remove install-sh #160 (andrewjpage)
- Debian bug 807150 #158 (andrewjpage)
v1.4.4 (2015-12-09)
v1.4.3 (2015-11-19)
Closed issues:
- multithreading #151
v1.4.2 (2015-09-02)
Merged pull requests:
- check for input files which are too long #153 (andrewjpage)
- update install docs #150 (andrewjpage)
v1.4.1 (2015-07-07)
v1.4.0 (2015-07-01)
Closed issues:
- "Binary package - For 64 bit Linux" links to nowhere #142
- INSTALL file not obvious #129
- segmentation fault #49
Merged pull requests:
- Convert python to 3 #149 (andrewjpage)
- update raxml version for travis #148 (andrewjpage)
- Add build status to README #147 (bewt85)
- Add TravisCI support #146 (bewt85)
- Reference URL updated to final published version not early access #145 (aslett1)
- Manually merge Aidan Delaneys pull request #144 (andrewjpage)
- Detect blocks at end of sequence #143 (andrewjpage)
v1.3.4 (2015-05-18)
Closed issues:
- No ./configure in github - need to run autoconf? #130
v1.3.3 (2015-04-16)
Merged pull requests:
- Window size self error #140 (andrewjpage)
- Window size self error #139 (andrewjpage)
v1.3.1 (2015-04-16)
Merged pull requests:
- version 1.3.1 #138 (andrewjpage)
v1.3.0 (2015-04-16)
Merged pull requests:
- Recalculate genome length #137 (andrewjpage)
- Downstream recombinations #136 (andrewjpage)
v1.2.4 (2015-03-31)
Merged pull requests:
- output version in python script #135 (andrewjpage)
v1.2.3 (2015-03-30)
Merged pull requests:
- include last element of array #134 (andrewjpage)
v1.2.2 (2015-03-30)
v1.2.1 (2015-03-30)
Merged pull requests:
- Correct vcf format and EMBL format #133 (andrewjpage)
- debian changelog #132 (andrewjpage)
- Dont fill in gaps in parent with bases from child #131 (andrewjpage)
v1.1.2 (2015-03-06)
v1.2.0 (2015-03-06)
Merged pull requests:
- Update robustness #128 (andrewjpage)
- message about invalid outgroups #127 (andrewjpage)
v1.1.1 (2015-01-23)
Merged pull requests:
- Clade as outgroup #126 (andrewjpage)
v1.1.0 (2015-01-23)
v1.0.12 (2015-01-20)
Merged pull requests:
- test data #125 (andrewjpage)
- Remove internal nodes from final tree #124 (andrewjpage)
v1.0.11 (2015-01-19)
Merged pull requests:
- check fasta files valid and check for intermediate raxml files #123 (andrewjpage)
v1.0.10 (2015-01-19)
v1.0.9 (2015-01-06)
1.0.9 (2015-01-06)
Merged pull requests:
- Dont use cpu info to find the flags #122 (andrewjpage)
- class namespace #121 (andrewjpage)
v1.0.8 (2014-12-08)
Merged pull requests:
- reduced functionality but more stable cpu info lookup #120 (andrewjpage)
- Rho theta #119 (andrewjpage)
v1.0.7 (2014-12-08)
Merged pull requests:
- allow for variation and exclude zero track length #118 (andrewjpage)
v1.0.6 (2014-12-03)
v1.0.5 (2014-11-19)
Merged pull requests:
- fasttree executables with titlecase and lowercase #117 (andrewjpage)
- warning message when changing number of threads #116 (andrewjpage)
- Change raxml exec search order #115 (andrewjpage)
v1.0.2 (2014-10-16)
Merged pull requests:
- rename convergence methods and allow for more #114 (andrewjpage)
v1.0.1 (2014-10-14)
Merged pull requests:
- unstable test fixed #113 (andrewjpage)
v1.0 (2014-10-14)
Merged pull requests:
- Converging recombinations #112 (andrewjpage)
0.7 (2014-09-24)
0.6 (2014-09-24)
v0.6 (2014-09-09)
Merged pull requests:
- Gubbins drawer can use recombination embl file #111 (andrewjpage)
v0.5 (2014-09-09)
Merged pull requests:
- thread support for raxml #110 (andrewjpage)
v0.4.1 (2014-09-08)
Merged pull requests:
- Check for lowercase fasttree exec #109 (andrewjpage)
v0.4 (2014-09-05)
Merged pull requests:
- pairwise rename output files #108 (andrewjpage)
- Update stats headers #107 (andrewjpage)
v0.3 (2014-09-04)
0.2 (2014-09-02)
Merged pull requests:
- Catch too few sequences #106 (andrewjpage)
0.1.11 (2014-08-22)
Merged pull requests:
- version in configure #105 (andrewjpage)
- Support for bipartition trees as input #104 (andrewjpage)
0.1.10 (2014-08-22)
Merged pull requests:
- print list of excluded sequences #103 (andrewjpage)
0.1.9 (2014-08-22)
Merged pull requests:
- print errors for invalid input files #102 (andrewjpage)
0.1.8 (2014-08-15)
Merged pull requests:
- Fasttree exec #101 (andrewjpage)
0.1.7 (2014-08-14)
Merged pull requests:
- Build for trusty #100 (andrewjpage)
0.1.6 (2014-08-12)
Merged pull requests:
- Changes from Aidan Delaney #99 (andrewjpage)
- Stats missing snps #98 (andrewjpage)
- update no support option in fastml #97 (andrewjpage)
- move blocks inwards #96 (andrewjpage)
- define is starting tree method as static #95 (andrewjpage)
- starting tree needed to come from args #94 (andrewjpage)
- Python tests #93 (andrewjpage)
- remove duplicate move #92 (andrewjpage)
- dont move in twice #91 (andrewjpage)
- typo in method, too many args #90 (andrewjpage)
- move end block in correct number of snps #89 (andrewjpage)
- Span gaps #88 (andrewjpage)
- translate snps and gaps to original genome space coords #87 (andrewjpage)
- extend blocks over gaps #86 (andrewjpage)
- dont call methods and variables the same thing #85 (andrewjpage)
- remove latest tree symlink if it exists, even if its broken #84 (andrewjpage)
- delete intermediate raxml files #83 (andrewjpage)
- Eliminate memory leaks and uninitalised reads/writes #82 (andrewjpage)
- GPL #81 (andrewjpage)
- reduce memory usage and fix seg fault #80 (andrewjpage)
- move math lib linking to end #79 (andrewjpage)
- move zlib linking to end #78 (andrewjpage)
- swap output suppression #77 (andrewjpage)
- memory leaks #76 (andrewjpage)
- update window creation #75 (andrewjpage)
- part4 log10 #74 (andrewjpage)
- Improving likelihood #73 (andrewjpage)
- Improving likelihood #72 (andrewjpage)
- reroot on outgroup should keep internal nodes #71 (andrewjpage)
- Use bases for gaps for internal nodes after fastml #70 (andrewjpage)
- propagate unambiguous bases up the tree #69 (andrewjpage)
- move inwards one at a time, remove gap extending, Bonferroni correction, sliding window 1 #68 (andrewjpage)
- new window shifting method and bug with detecting snps #67 (andrewjpage)
- dont move window past size of genome #66 (andrewjpage)
- move window in to first snp #65 (andrewjpage)
- Updates to coords other minor bugs #64 (andrewjpage)
- sliding window at half minimum window size #63 (andrewjpage)
- swap bases in snp tab file and cleanup filenames #62 (andrewjpage)
- Gaps can be in ref as well as alt #61 (andrewjpage)
- pairwise #60 (andrewjpage)
- remove filtered sequences from starting tree #59 (andrewjpage)
- missing comma #58 (andrewjpage)
- unquote tree nodes for fastml and check if too much is filtered out #57 (andrewjpage)
- update test files #56 (andrewjpage)
- Fastml no gaps #55 (andrewjpage)
- readme #54 (andrewjpage)
- snp branch output and prefiltering aln #53 (andrewjpage)
- make drawer work with empty tracks #52 (andrewjpage)
- strip off input params when testing if exec is in path #51 (andrewjpage)
- Fastml integration #50 (andrewjpage)
- versioning #48 (andrewjpage)
- Cleanup intermediate files #47 (andrewjpage)
- treat N in the same way as gaps when snp searching #46 (andrewjpage)
- Treat N as gap when extending over gaps at block boundries #45 (andrewjpage)
- use same fasttree params in hybrid #44 (andrewjpage)
- vcf coords start from 1 #43 (andrewjpage)
- unquote strings #42 (andrewjpage)
- default preserve underscores to true #41 (andrewjpage)
- preserve underscores #40 (andrewjpage)
- Reroot around edge #39 (andrewjpage)
- remove calls to reading beginnign of line #38 (andrewjpage)
- Read line memory leak #37 (andrewjpage)
- increase read line memory #36 (andrewjpage)
- resize read line buffer #35 (andrewjpage)
- Copyfile #34 (andrewjpage)
- increase read buffer size #33 (andrewjpage)
- semi colon at end of tree #32 (andrewjpage)
- speedup gubbins #31 (andrewjpage)
- scale distances by num snps #30 (andrewjpage)
- providing a starting tree skips first tree building step #29 (andrewjpage)
- calc bases in recombs #28 (andrewjpage)
- improved stats #27 (andrewjpage)
- calc snp stats and parameter to set min snps #26 (andrewjpage)
- Get all gaps #25 (andrewjpage)
- increase window size to 20k #24 (andrewjpage)
- Span gaps #23 (andrewjpage)
- fasttree needs to use output of gubbins #22 (andrewjpage)
- extend blocks over gaps #21 (andrewjpage)
- raxml exec check #20 (andrewjpage)
- Merge blocks straddling gaps #19 (andrewjpage)
- fix remove #18 (andrewjpage)
- speedup phylip file writing second try #17 (andrewjpage)
- speedup phylip file writing #16 (andrewjpage)
- provide alignment filename not full path for fastree #15 (andrewjpage)
- remove hardcoded path to exec #14 (andrewjpage)
- rerun autoreconf #13 (andrewjpage)
- midpoint rerooting and pairwise comparison #12 (andrewjpage)
- Use get opt long #11 (andrewjpage)
- dont point to gubbins in same dir #10 (andrewjpage)
- dont print out rerooted tree to stdout #9 (andrewjpage)
- Hybrid tree building #8 (andrewjpage)
- Rewrite perl as python #7 (andrewjpage)
- send in most recent phylip file to raxml #6 (andrewjpage)
- run gubbins original snp sites #5 (andrewjpage)
- run gubbins with original snp sites #4 (andrewjpage)
- Gubbins overall tests #3 (andrewjpage)
- Fix memory leak and properly remove recombinations #2 (andrewjpage)
- dont ignore internal nodes #1 (andrewjpage)
* This Change Log was automatically generated by github_changelog_generator