Commits · pantools_v3 · bioinformatics / PanTools

01 Dec, 2022 1 commit
- Merge branch 'release' into 'pantools_v3' · 5f8671bc
  Workum, Dirk-Jan van authored Dec 01, 2022
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Release v3.4.0

Closes #1, #2, #4, #5, #16, and #9

See merge request !98
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  5f8671bc
29 Nov, 2022 4 commits
- remove old v3.4 jar from release branch · db71492e
  Workum, Dirk-Jan van authored Nov 29, 2022
  
  db71492e
- move getting pantools version to start of main method to always get the correct version of pantools · 1b205255
  Workum, Dirk-Jan van authored Nov 29, 2022
  
  1b205255
- update readme.md and install.md to v3.4.0 install and compile instructions · 2a4a7348
  Workum, Dirk-Jan van authored Nov 29, 2022
  
  2a4a7348
- forgot to update one location of v3.4 to v3.4.0 · 5018373b
  Workum, Dirk-Jan van authored Nov 29, 2022
  
  5018373b
28 Nov, 2022 4 commits
- change v3.4 to v3.4.0 and update pantools download instructions · 22657f20
  Workum, Dirk-Jan van authored Nov 28, 2022
  
  22657f20
- Merge branch 'pantools_v3.2' into pantools_v3 · 3dcdaf34
  Workum, Dirk-Jan van authored Nov 28, 2022
  
  3dcdaf34
- Merge branch 'pantools_v3.1' into pantools_v3 · e5f30dea
  Workum, Dirk-Jan van authored Nov 28, 2022
  
  e5f30dea
- deleted log · 4b27c1db
  Workum, Dirk-Jan van authored Nov 28, 2022
  
  4b27c1db
16 Nov, 2022 2 commits
- Merge branch 'pantools_v3.4' into 'release' · b5187df4
  Smit, Sandra authored Nov 16, 2022
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merge pantools_v3.4 with read the docs documentation to release

See merge request !90
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  b5187df4
- merge pantools_v3.4 with read the docs documentation to release · 0518d54a
  Esch, Roel van authored Nov 16, 2022 and Smit, Sandra committed Nov 16, 2022
  
  0518d54a
21 Oct, 2022 4 commits
- Merge branch 'pantools_v3.4' into 'release' · c484d8bc
  Lankveld, Thijs van authored Oct 21, 2022
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Pantools v3.4 to release

See merge request !84
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  c484d8bc
- Merge branch 'release' into 'pantools_v3.4' · d4269b01
  Lankveld, Thijs van authored Oct 21, 2022
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# Conflicts:
#   README.md
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  d4269b01
- Merge branch 'pantools_v3.2' into 'release' · a54a27b8
  Lankveld, Thijs van authored Oct 21, 2022
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Pantools v3.2 to release

See merge request !83
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  a54a27b8
- Merge branch 'pantools_v3.1' into 'release' · e2a57864
  Lankveld, Thijs van authored Oct 21, 2022
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Pantools v3.1 to release

See merge request !82
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  e2a57864
20 Jul, 2022 4 commits
- Merge branch 'interpro_download_v3.1' into 'pantools_v3.1' · 8a37d4b9
  Workum, Dirk-Jan van authored Jul 20, 2022
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Added script to download, check, and unpack interpro dataset.

See merge request !48
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  8a37d4b9
- Added script to download, check, and unpack interpro dataset. · a19ac60c
  Lankveld, Thijs van authored Jul 20, 2022 and Workum, Dirk-Jan van committed Jul 20, 2022
  
  a19ac60c
- Merge branch 'interpro_download_v3' into 'pantools_v3' · c9376adb
  Workum, Dirk-Jan van authored Jul 20, 2022
```
Added script to download, check, and unpack interpro dataset.

See merge request !47
```
  c9376adb
- Added script to download, check, and unpack interpro dataset. · 72efa1f1
  Lankveld, Thijs van authored Jul 20, 2022 and Workum, Dirk-Jan van committed Jul 20, 2022
  
  72efa1f1
14 Jul, 2022 1 commit
- Update CHANGELOG.md · 62c6a41a
  Jonkheer, Eef authored Jul 14, 2022
  
  62c6a41a
04 May, 2022 2 commits
- Include .jar file for release version · e2257e66
  Jonkheer, Eef authored May 04, 2022
  
  e2257e66
- Included option to bin numerical values in 'add_phenotype' · 046286b6
  Jonkheer, Eef authored May 04, 2022
  
  046286b6
03 May, 2022 1 commit
- 'rename_phylogeny' now takes the correct genome number in nexus files · e12be882
  Jonkheer, Eef authored May 03, 2022
  
  e12be882
24 Apr, 2022 1 commit
- 'Rename_phylogeny' now works on split tree files · 74559f92
  Jonkheer, Eef authored Apr 24, 2022
  
  74559f92
15 Apr, 2022 1 commit
- first steps made for 'rename_phylogeny' on split trees · b17161b6
  Jonkheer, Eef authored Apr 15, 2022
  
  b17161b6
06 Apr, 2022 4 commits
- merged to master · 027d2085
  Eef Jonkheer authored Apr 06, 2022
  
  027d2085
- uniquify_msa_headers fasta headers · 95371a4f
  Eef Jonkheer authored Apr 06, 2022
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Merge branch 'master' of https://git.wur.nl/bioinformatics/pantools
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  95371a4f
- Merge branch 'uniquify_msa_headers' into 'master' · 1afdc26d
  Workum, Dirk-Jan van authored Apr 06, 2022
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removing identifiers_incorrect_for_fasttree and uniquifying all sequences that are input for MSA

See merge request !39
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  1afdc26d
- removing identifiers_incorrect_for_fasttree and uniquifying all sequences that are input for MSA · 9cdfa626
  Workum, Dirk-Jan van authored Apr 06, 2022
  
  9cdfa626
05 Apr, 2022 2 commits
- Updated ggplot colours with colourblind-friendly palette · 2a8579ba
  Eef Jonkheer authored Apr 05, 2022
  
  2a8579ba
- Updated ggplot colours with colourblind-friendly palette · 1314a6d1
  Eef Jonkheer authored Apr 05, 2022
  
  1314a6d1
29 Mar, 2022 2 commits
- Merge branch 'consensus_tree_no_polytomies' into 'master' · ac129698
  Workum, Dirk-Jan van authored Mar 29, 2022
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make ignoring of polytomies default for ASTRAL-PRO

See merge request !37
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  ac129698
- make ignoring of polytomies default for ASTRAL-PRO · c77d2a06
  Workum, Dirk-Jan van authored Mar 29, 2022
  
  c77d2a06
25 Mar, 2022 1 commit
- Merge branch 'high_freq_kmer_classification' into 'master' · 9d318ee3
  Jonkheer, Eef authored Mar 25, 2022
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High freq kmer classification

See merge request !36
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  9d318ee3
21 Mar, 2022 2 commits
- Resolved an issue where generated to many warnings · 460be8f3
  Eef Jonkheer authored Mar 21, 2022
  
  460be8f3
- Merge branch 'master' into high_freq_kmer_classification · a7216a0c
  Eef Jonkheer authored Mar 21, 2022
  
  a7216a0c
18 Mar, 2022 1 commit
- Merge branch 'hotfix_core_snp_tree' into 'master' · f2d9e35a
  Workum, Dirk-Jan van authored Mar 18, 2022
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let core_snp_tree search for alignment with updated msaNames variable instead...

See merge request !35
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  f2d9e35a
17 Mar, 2022 1 commit
- let core_snp_tree and consensus_tree print progress · 9cfb6eec
  Workum, Dirk-Jan van authored Mar 17, 2022
  
  9cfb6eec
14 Mar, 2022 1 commit
- let core_snp_tree search for alignment with updated msaNames variable instead... · a0b7bf0e
  Workum, Dirk-Jan van authored Mar 14, 2022
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let core_snp_tree search for alignment with updated msaNames variable instead of not updated hmNodeList
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  a0b7bf0e
09 Mar, 2022 1 commit
- Merge branch 'add_fasttree_options_to_msa' into 'master' · 15c9d876
  Workum, Dirk-Jan van authored Mar 09, 2022
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small improvement to running fasttree

See merge request !34
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  15c9d876