Commits · 9c9ddd3bdf93c2712a83516f1c536c5cd2e73c88 · VEBER Philippe / codepi

06 Feb, 2020 1 commit
- update wrt world · 9c9ddd3b
  Philippe Veber authored Feb 06, 2020
  
  9c9ddd3b
13 Dec, 2019 1 commit
- update wrt phylogenetics and bistro · a3df223f
  Philippe Veber authored Dec 13, 2019
  
  a3df223f
08 Nov, 2019 1 commit
- add pcoc_v2 (V1 implementation with C10/C60 + manual profils with V1 implementation) · e5695953
  Carine Rey authored Nov 08, 2019
  
  e5695953
09 Oct, 2019 2 commits
- add option --dnds (calc dn ds dn/ds trees; add option --gt (calc gene trees) · 02b0d86b
  Carine Rey authored Oct 09, 2019
  
  02b0d86b
- Add gene tree building using raxmlng · ca2ce705
  Carine Rey authored Oct 09, 2019
  
  ca2ce705
08 Oct, 2019 1 commit
- realdata: add a output repo with parsed input files · 91b4df22
  Carine Rey authored Oct 08, 2019
  
  91b4df22
27 Sep, 2019 3 commits
- New module Real_dataset: pipeline for real datasets! · ac2adfb0
  Philippe Veber authored Sep 27, 2019
  
  ac2adfb0
- Pipeline refactoring (added functor) · 7b241068
  Philippe Veber authored Sep 27, 2019
  
  7b241068
- Parse_input_tree.py : split file to remove dependencies · ff0000aa
  Carine Rey authored Sep 27, 2019
  
  ff0000aa
20 Sep, 2019 19 commits
- fix compilation errors due to merge with master · 98eaf13c
  Philippe Veber authored Sep 20, 2019
  
  98eaf13c
- fix error · 7b42ed65
  Carine Rey authored Jun 19, 2019
  
  7b42ed65
- add indel cols if not pcoc · a4280494
  Carine Rey authored Jun 06, 2019
  
  a4280494
- rm time logger for real dataset · b034bd73
  Carine Rey authored Jun 05, 2019
  
  b034bd73
- rm plot · 88eb2f70
  Carine Rey authored Jun 05, 2019
  
  88eb2f70
- fix error during tree pruning · 8d3f4472
  Carine Rey authored Jun 05, 2019
  
  8d3f4472
- comment useless methods · 987009b7
  Carine Rey authored May 13, 2019
  
  987009b7
- typo · 7fa12544
  Carine Rey authored Apr 01, 2019
  
  7fa12544
- add calc_dnds · 4b3ad11d
  Carine Rey authored Apr 01, 2019
  
  4b3ad11d
- add input for diffsel in realdata dataset output · 4fd11201
  Carine Rey authored Jan 22, 2019
  
  4fd11201
- add faa in output · c0d4872d
  Carine Rey authored Jan 18, 2019
  
  c0d4872d
- add pcoc with max_gap_allowed · 29f00885
  Carine Rey authored Jan 16, 2019
  
  29f00885
- add --max_gap_allowed --max_gap_allowed_in_conv_leaves · bc1d0938
  Carine Rey authored Jan 16, 2019
  
  bc1d0938
- add descr · bc830089
  Carine Rey authored Jan 16, 2019
  
  bc830089
- fix error · e23b62a6
  Carine Rey authored Jan 16, 2019
  
  e23b62a6
- auto rm leaves if lacking sequences · f99b6287
  Carine Rey authored Jan 15, 2019
  
  f99b6287
- add model in descr in pcoc and tdg09 · e9b996b3
  Carine Rey authored Jan 15, 2019
  
  e9b996b3
- add tests · 0e43ad72
  Carine Rey authored Jan 15, 2019
  
  0e43ad72
- change realdata inputdir tree · 35a594d0
  Carine Rey authored Jan 15, 2019
  
  35a594d0
17 Jul, 2019 5 commits
- Fixed error in expected gc quantiles · 143c7e29
  LANORE Vincent authored Jul 17, 2019
  
  143c7e29
- Realism filter now uses convergent gc content instead of global · d4872dac
  LANORE Vincent authored Jul 17, 2019
  
  d4872dac
- Added new realistic filter with gc content mean quantiles · 9589905d
  LANORE Vincent authored Jul 17, 2019
  
  9589905d
- refactoring: started toolbox library · 138f2ee4
  Philippe Veber authored Jul 17, 2019
```
toolbox will be used to separate simple ocaml functions from bistro
workflows.
```
  138f2ee4
- Alistats: added convergent/ancestral differentiated GC computation · 5d16d54d
  Philippe Veber authored Jul 17, 2019
  
  5d16d54d
16 Jul, 2019 7 commits
- Simulator: produce histogram of fitness values · 8cb49aff
  Philippe Veber authored Jul 16, 2019
  
  8cb49aff
- Simulator: fixed serious bug · e43517ef
  Philippe Veber authored Jul 16, 2019
```
the parameters used for root distribution and site evolution used to
be different, because of unwanted repeated sampling. That's what you
get using impure functions.
```
  e43517ef
- Alistat.nucleotide_fasta_gc: compute GC stats at any pos in codon · 7df238ca
  Philippe Veber authored Jul 16, 2019
  
  7df238ca
- Added filtering functions + random refactoring of exploration things · bb8a7d46
  LANORE Vincent authored Jul 16, 2019
  
  bb8a7d46
- Added basic infrastructure for param exploration · 9c63ef86
  LANORE Vincent authored Jul 16, 2019
  
  9c63ef86
- Alistat.nucleotide_fasta_gc: compute inter sequence variance · 742207bf
  Philippe Veber authored Jul 16, 2019
  
  742207bf
- Pipeline2: added OCaml impl of R/P curve · 58668233
  Philippe Veber authored Jul 16, 2019
  
  58668233