Commits · master · ORG.Asm / ORG.Annotate

08 Nov, 2021 3 commits
- Update README.md to list every nix packages corresponding to org.annot dependences · 12c47ebe
  Eric Coissac authored Nov 08, 2021
  
  12c47ebe
- Update README.txt name to `.md` · 9b7bbd04
  Eric Coissac authored Nov 08, 2021
  
  9b7bbd04
- Update README.txt to switch to Markdown format · 62b25584
  Eric Coissac authored Nov 08, 2021
  
  62b25584
05 Nov, 2021 2 commits
- Makes modification on the sequence header and feature source · 10e92164
  Eric Coissac authored Nov 05, 2021
  
  10e92164
- change tRNA and CDS annotations · 12b6c560
  Eric Coissac authored Nov 05, 2021
  
  12b6c560
04 Nov, 2021 5 commits
- Patch the name of rRNA genes · ba00e56f
  Eric Coissac authored Nov 04, 2021
  
  ba00e56f
- Adds changes to conform with EMBL template files · 93da2c4c
  Eric Coissac authored Nov 04, 2021
  
  93da2c4c
- Patch the detection algorithm (the overlap detection) · 7aca679a
  Eric Coissac authored Nov 04, 2021
  
  7aca679a
- Adds new options and call the new bash version of go_cds · 2489ee1f
  Eric Coissac authored Nov 04, 2021
  
  2489ee1f
- Switch the go_cds script from tcsh to bash · 36041f96
  Eric Coissac authored Nov 04, 2021
  
  36041f96
03 Nov, 2021 2 commits
- Small indentation change · 65aab588
  Eric Coissac authored Nov 03, 2021
  
  65aab588
- Adds the detection of the RPS12 gene (Gene with trans-splicing) · 2396df18
  Eric Coissac authored Nov 03, 2021
  
  2396df18
01 Jun, 2021 2 commits
- Adds options to allows to disconnect some detectors · bcaea43d
  Eric Coissac authored Jun 01, 2021
  
  bcaea43d
- Move the script used for clusterizing protein DBs · c27edd09
  Eric Coissac authored Jun 01, 2021
  
  c27edd09
05 Apr, 2019 1 commit
- add a -l option to set a minimum length on the contig to annotate · a16feefc
  Eric Coissac authored Apr 05, 2019
  
  a16feefc
20 Nov, 2018 4 commits
- Patch a bug leading to a double pseudogene tagging · 35e27b66
  Eric Coissac authored Nov 20, 2018
  
  35e27b66
- If proteins are looked for without stop adds an extra option · 318327af
  Eric Coissac authored Nov 20, 2018
```
PASS1_LOOK_FOR_PSEUDO allowing for searching with stop in a second time
(Pseudogene search).

The PASS1_ALLOW_STOP is set back to 0 and the new PASS1_LOOK_FOR_PSEUDO
is set to 1
```
  318327af
- Check the translation for stop codon and add a pseudogene qualifier if · 11b612fc
  Eric Coissac authored Nov 20, 2018
```
present.
```
  11b612fc
- Merge branch 'master' of ssh://git@git.metabarcoding.org/org-asm/org-annotate.git · 0eee2e07
  Eric Coissac authored Nov 20, 2018
  
  0eee2e07
11 May, 2018 5 commits
- Add .DS_Store to the .gitignore files · b92f4196
  Eric Coissac authored May 11, 2018
  
  b92f4196
- Add .DS_Store to the .gitignore files · a543c30e
  Eric Coissac authored May 11, 2018
  
  a543c30e
- Correct .gitignore files · 9d27bea3
  Eric Coissac authored May 11, 2018
  
  9d27bea3
- Redirect output of pushd and popd to /dev/null · e6ce2c73
  Eric Coissac authored May 11, 2018
  
  e6ce2c73
- Switch to version 2.4.0 of exonerate · c3d1cd54
  Eric Coissac authored May 11, 2018
  
  c3d1cd54
05 Apr, 2018 9 commits
- Freshly regerenrated CAU tRNA reference library with the new tool script · b2808b9d
  Eric Coissac authored Apr 05, 2018
  
  b2808b9d
- Add eclipse project files · 96afe525
  Eric Coissac authored Apr 05, 2018
  
  96afe525
- Changes in .gitignore · 7e9fcd4e
  Eric Coissac authored Apr 05, 2018
  
  7e9fcd4e
- Switch to clustal-omega version 1.2.4 · f2eba5fb
  Eric Coissac authored Apr 05, 2018
  
  f2eba5fb
- Switch to version 1.2.38 of aragorn · 8fdde2e7
  Eric Coissac authored Apr 05, 2018
  
  8fdde2e7
- Change the notation algorithm to take advantage of the new CAU tRNA · 32650f41
  Eric Coissac authored Apr 05, 2018
```
reference library
```
  32650f41
- Modify script to accept compressed genome files · f816e3ce
  Eric Coissac authored Apr 05, 2018
  
  f816e3ce
- New version of the CAU tRNA reference database · 15ec72ca
  Eric Coissac authored Apr 05, 2018
  
  15ec72ca
- Simplify CAU tRNA reference database building to keep onlyCAU tRNA · 67dc4456
  Eric Coissac authored Apr 05, 2018
```
from plastomes where the three categories of CAU tRNA (Met/Ile/fMet)
are annotated
```
  67dc4456
30 Mar, 2018 2 commits
- Switch to clustalo version 1.2.4 · 0e15ea20
  Eric Coissac authored Mar 30, 2018
  
  0e15ea20
- Switch Aragorn to version 1.2.38 · 46bb3669
  Eric Coissac authored Mar 30, 2018
  
  46bb3669
25 Jan, 2018 1 commit
- Final small changes to patch the bug related to complex filenames · c59d7b5e
  Eric Coissac authored Jan 25, 2018
  
  c59d7b5e
24 Jan, 2018 4 commits
- Always a new attempt to solve the bug... · 0a5ece1e
  Eric Coissac authored Jan 24, 2018
  
  0a5ece1e
- Comment out phase 2 CDS searching · ca048f8c
  Eric Coissac authored Jan 24, 2018
  
  ca048f8c
- Add missing file... · f71b0396
  Eric Coissac authored Jan 24, 2018
  
  f71b0396
- Merge branch 'master' of · aeae3d48
  Eric Coissac authored Jan 24, 2018
```
ssh://git@git.metabarcoding.org/org-asm/org-annotate.git

Conflicts:
	detectors/cds/bin/do_exonerate.csh
```
  aeae3d48