Commits · fa0dfd7235bb0c214c4e2ffd7a18ea99a4218a6c · phylo / fastcodeml

28 Jan, 2013 1 commit

Changed variable initialization logic. · fa0dfd72

mvalle authored Jan 28, 2013

Implemented initialize h0 from h1 also for MPI.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5831 95c5a404-1f88-0410-a6b0-c3f062b6f34a

fa0dfd72

24 Jan, 2013 3 commits

Fixed doxygen comments. · c99c26c9

mvalle authored Jan 24, 2013


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5813 95c5a404-1f88-0410-a6b0-c3f062b6f34a

c99c26c9

Fixed various typos in doxygen comments and in two exception messages. · 94715e19

mvalle authored Jan 24, 2013


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5812 95c5a404-1f88-0410-a6b0-c3f062b6f34a

94715e19

Updated doxygen to 1.8.3.1 · 0d0f30a0

mvalle authored Jan 24, 2013

Added switches to compute a range of branches
Added branch selection (single branch or range of branches) to MPI.

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5809 95c5a404-1f88-0410-a6b0-c3f062b6f34a

0d0f30a0

18 Jan, 2013 1 commit

Minor improvements to code and comments · 38c02be3

mvalle authored Jan 18, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5752 95c5a404-1f88-0410-a6b0-c3f062b6f34a

38c02be3

17 Jan, 2013 1 commit

Corrected gap/ambiguous positions discovery. · 87e32b97

mvalle authored Jan 17, 2013

Added test for invalid root configurations.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5745 95c5a404-1f88-0410-a6b0-c3f062b6f34a

87e32b97

15 Jan, 2013 2 commits

· ec3a20ec

hschabau authored Jan 15, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5711 95c5a404-1f88-0410-a6b0-c3f062b6f34a

ec3a20ec

Fixed read for specific msa (specie name alone on a line) · 736673e2

mvalle authored Jan 15, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5704 95c5a404-1f88-0410-a6b0-c3f062b6f34a

736673e2

14 Jan, 2013 1 commit

Restricted Doxygen to *.h and *.cpp files · 58c7c0a0

mvalle authored Jan 14, 2013

Now ignore empty lines at the beginning of the msa
Added routine to check the branches on the tree root.

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5673 95c5a404-1f88-0410-a6b0-c3f062b6f34a

58c7c0a0

11 Jan, 2013 3 commits

Fixed Doxyfile. Fixed Doxygen comment in source. · 20c6890a

mvalle authored Jan 11, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5669 95c5a404-1f88-0410-a6b0-c3f062b6f34a

20c6890a

Corrected comment · f509e265

mvalle authored Jan 11, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5660 95c5a404-1f88-0410-a6b0-c3f062b6f34a

f509e265

Added check for no internal branches · 88257242

mvalle authored Jan 11, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5659 95c5a404-1f88-0410-a6b0-c3f062b6f34a

88257242

10 Jan, 2013 1 commit

Removed commented code · a8f82c78

mvalle authored Jan 10, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5653 95c5a404-1f88-0410-a6b0-c3f062b6f34a

a8f82c78

08 Jan, 2013 1 commit

Print and remove gaps. Print num of ambiguous sites · 00b3dbc0

mvalle authored Jan 08, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5636 95c5a404-1f88-0410-a6b0-c3f062b6f34a

00b3dbc0

07 Jan, 2013 2 commits

cleaning up · 86c0668f

hschabau authored Jan 07, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5635 95c5a404-1f88-0410-a6b0-c3f062b6f34a

86c0668f

Changed LRT print format for MPI · d829690e

mvalle authored Jan 07, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5634 95c5a404-1f88-0410-a6b0-c3f062b6f34a

d829690e

02 Jan, 2013 1 commit

Added variable print also for MPI · f8586a87

mvalle authored Jan 02, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5633 95c5a404-1f88-0410-a6b0-c3f062b6f34a

f8586a87

28 Dec, 2012 1 commit
- Remove spaces from newick tree before parsing (the parser cannot cope with them) · f25a92bd
  mvalle authored Dec 28, 2012
```
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5632 95c5a404-1f88-0410-a6b0-c3f062b6f34a
```
  f25a92bd
24 Dec, 2012 1 commit

On ambiguous codons initialize leaves to 1/n_codons · 84ebf573

mvalle authored Dec 24, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5631 95c5a404-1f88-0410-a6b0-c3f062b6f34a

84ebf573

21 Dec, 2012 1 commit

Moved to main the check for null branch lengths from file. · da40b5aa

mvalle authored Dec 21, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5601 95c5a404-1f88-0410-a6b0-c3f062b6f34a

da40b5aa

19 Dec, 2012 4 commits

Corrected message silencing for MPI version. · 8d4fe618

mvalle authored Dec 19, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5571 95c5a404-1f88-0410-a6b0-c3f062b6f34a

8d4fe618

Print annotated tree with the internal branch number. · 82d4e2bc

mvalle authored Dec 19, 2012

Changed name to the internal variable mTimesFromFile to mBranchLengthFromFile.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5567 95c5a404-1f88-0410-a6b0-c3f062b6f34a

82d4e2bc

Fixed messages from MPI execution. · 3b7e20cb

mvalle authored Dec 19, 2012

Added LRT output from MPI execution.
Readded --times-from-file to support old scripts.

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5556 95c5a404-1f88-0410-a6b0-c3f062b6f34a

3b7e20cb

Added print of the LRT value · 9d0d0871

mvalle authored Dec 19, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5554 95c5a404-1f88-0410-a6b0-c3f062b6f34a

9d0d0871

18 Dec, 2012 1 commit

· ee1c914d

hschabau authored Dec 18, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5517 95c5a404-1f88-0410-a6b0-c3f062b6f34a

ee1c914d

15 Dec, 2012 1 commit

Ordered output sites under positive selection. · 5471b672

mvalle authored Dec 15, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5494 95c5a404-1f88-0410-a6b0-c3f062b6f34a

5471b672

13 Dec, 2012 1 commit

Changed option --times-from-file to --lenghts-from-file · dd310797

mvalle authored Dec 13, 2012

Changed gene file to alignment file.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5470 95c5a404-1f88-0410-a6b0-c3f062b6f34a

dd310797

12 Dec, 2012 1 commit

Changed message output to cout from cerr. · ee5c527a

mvalle authored Dec 12, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5413 95c5a404-1f88-0410-a6b0-c3f062b6f34a

ee5c527a

11 Dec, 2012 2 commits

Fixed problem with ambiguous codons. · ad0c251f

mvalle authored Dec 11, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5407 95c5a404-1f88-0410-a6b0-c3f062b6f34a

ad0c251f

added paths for dev · 67cb81bc

hschabau authored Dec 11, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5394 95c5a404-1f88-0410-a6b0-c3f062b6f34a

67cb81bc

06 Dec, 2012 3 commits

Changed output of sites under positive selection so the site number starts from 1 and not zero. · a021808c
mvalle authored Dec 06, 2012
```
git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5347 95c5a404-1f88-0410-a6b0-c3f062b6f34a
```
a021808c

Restructured few error messages. · 064a0a48

mvalle authored Dec 06, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5344 95c5a404-1f88-0410-a6b0-c3f062b6f34a

064a0a48

Added print num internal branches · 40acf8ea

mvalle authored Dec 06, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5343 95c5a404-1f88-0410-a6b0-c3f062b6f34a

40acf8ea

05 Dec, 2012 2 commits

· 98bf503e

hschabau authored Dec 05, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5333 95c5a404-1f88-0410-a6b0-c3f062b6f34a

98bf503e

· af416431

hschabau authored Dec 05, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5331 95c5a404-1f88-0410-a6b0-c3f062b6f34a

af416431

04 Dec, 2012 3 commits

Added print parameters. · a1a6de2f

mvalle authored Dec 04, 2012

Changed messages from Tree balancing.
Changed few BEB message formats.

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5328 95c5a404-1f88-0410-a6b0-c3f062b6f34a

a1a6de2f

Changed variable name conflicting with reserved word · 6ca0ee3e

mvalle authored Dec 04, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5327 95c5a404-1f88-0410-a6b0-c3f062b6f34a

6ca0ee3e

Changed newick grammar to accept species names starting with number. · 7b82e33e

mvalle authored Dec 04, 2012

Better error message in parsing trees.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5324 95c5a404-1f88-0410-a6b0-c3f062b6f34a

7b82e33e

03 Dec, 2012 1 commit

Fixed bug that appears in beb only using -nr flag. · 2d27a5b2

mvalle authored Dec 03, 2012


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5303 95c5a404-1f88-0410-a6b0-c3f062b6f34a

2d27a5b2

01 Dec, 2012 1 commit

generated mpi version for castor · 31f394a2

hschabau authored Dec 01, 2012

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5289 95c5a404-1f88-0410-a6b0-c3f062b6f34a

31f394a2