Commits · 94b0ddc063532cb8e8502cf0ad4310b4754236c4 · phylo / fastcodeml

17 Dec, 2013 1 commit

Add number_threads + change output file · 94b0ddc0

akalantz authored Dec 17, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@7105 95c5a404-1f88-0410-a6b0-c3f062b6f34a

94b0ddc0

16 Dec, 2013 3 commits

Add the unrooted tree (unrooted by NewickUtilities) as example because branch... · 6a05a0a8

smoretti authored Dec 16, 2013

Add the unrooted tree (unrooted by NewickUtilities) as example because branch lengths are much more stable this way, even in original codeml code

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@7092 95c5a404-1f88-0410-a6b0-c3f062b6f34a

6a05a0a8

Add the README file from the package + basic example files · aad6fb95

smoretti authored Dec 16, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@7091 95c5a404-1f88-0410-a6b0-c3f062b6f34a

aad6fb95

Rename former README as INSTALL · 8d9e0628

smoretti authored Dec 16, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@7090 95c5a404-1f88-0410-a6b0-c3f062b6f34a

8d9e0628

02 Jul, 2013 1 commit

cleaning up · 44f69dc4

hschabau authored Jul 02, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6849 95c5a404-1f88-0410-a6b0-c3f062b6f34a

44f69dc4

20 Jun, 2013 1 commit

finishing fastcodeml paper submission · e215432f

hschabau authored Jun 20, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6807 95c5a404-1f88-0410-a6b0-c3f062b6f34a

e215432f

04 Jun, 2013 1 commit

· 0674fa2e

hschabau authored Jun 04, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6616 95c5a404-1f88-0410-a6b0-c3f062b6f34a

0674fa2e

29 May, 2013 1 commit

Added exception for LRT not satisfied. · 64f47277

mvalle authored May 29, 2013

Added maximization stop after given number of iterations.
Added new cmd line options to define maximum number of iterations.

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6593 95c5a404-1f88-0410-a6b0-c3f062b6f34a

64f47277

15 May, 2013 2 commits

added epflcpt15 installation settings · 9bd7b64a

hschabau authored May 15, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6554 95c5a404-1f88-0410-a6b0-c3f062b6f34a

9bd7b64a

Clarified comments. · 3f15b4e8

mvalle authored May 15, 2013

Removed possible race in variable initialization.
Don't change vars if they come from H1.

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6553 95c5a404-1f88-0410-a6b0-c3f062b6f34a

3f15b4e8

30 Apr, 2013 2 commits

Added comments. Cleaned few datatypes · c96fbb3d

mvalle authored Apr 30, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6497 95c5a404-1f88-0410-a6b0-c3f062b6f34a

c96fbb3d

Changed exception that ends optimization in the event of LRT not satisfied · 1657c884

mvalle authored Apr 30, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6495 95c5a404-1f88-0410-a6b0-c3f062b6f34a

1657c884

26 Apr, 2013 4 commits

Fixed print bug in m22. · d2d46ac2

mvalle authored Apr 26, 2013

Added line breaks in trace print.
More room added for codon counts in Codon Frequencies.

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6478 95c5a404-1f88-0410-a6b0-c3f062b6f34a

d2d46ac2

fixed cut and paste error · 34f46eff

mvalle authored Apr 26, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6472 95c5a404-1f88-0410-a6b0-c3f062b6f34a

34f46eff

Renamed constant to reflect the program logic · c4ac4001

mvalle authored Apr 26, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6468 95c5a404-1f88-0410-a6b0-c3f062b6f34a

c4ac4001

Changed initialization of variables to be like it is done in CodeML. · bbd7141e

mvalle authored Apr 26, 2013

Same for constraining variables inside search domain.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6467 95c5a404-1f88-0410-a6b0-c3f062b6f34a

bbd7141e

25 Apr, 2013 1 commit

Added codon frequency table print connected to the verbose value. · 9ec41ac4

mvalle authored Apr 25, 2013

Now fixed leaves initialization to 1


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6456 95c5a404-1f88-0410-a6b0-c3f062b6f34a

9ec41ac4

24 Apr, 2013 1 commit

Fixed codon frequencies calculation for ambiguous codons · 7c30fd34

mvalle authored Apr 24, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6444 95c5a404-1f88-0410-a6b0-c3f062b6f34a

7c30fd34

23 Apr, 2013 1 commit

Unify codon frequencies print format with CodeML, start attaching ambiguous... · cf964c42

mvalle authored Apr 23, 2013

Unify codon frequencies print format with CodeML, start attaching ambiguous codon computation of codon frequencies

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6434 95c5a404-1f88-0410-a6b0-c3f062b6f34a

cf964c42

22 Apr, 2013 2 commits

Removed printing of codon empirical frequencies · 587f1e08

mvalle authored Apr 22, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6422 95c5a404-1f88-0410-a6b0-c3f062b6f34a

587f1e08

Fixed case with codon frequencies equal zero · bf00228f

mvalle authored Apr 22, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6420 95c5a404-1f88-0410-a6b0-c3f062b6f34a

bf00228f

16 Apr, 2013 2 commits

Implemented codon frequency estimation for ambiguous data as in CodeML · 9df18794

mvalle authored Apr 16, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6394 95c5a404-1f88-0410-a6b0-c3f062b6f34a

9df18794

Added compile option for totally ambiguous codon all one · c96acc3d

mvalle authored Apr 16, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6393 95c5a404-1f88-0410-a6b0-c3f062b6f34a

c96acc3d

10 Apr, 2013 1 commit

Added LRT optimization also to m22 optimizer · a8cdde25

mvalle authored Apr 10, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6337 95c5a404-1f88-0410-a6b0-c3f062b6f34a

a8cdde25

09 Apr, 2013 3 commits

update · 562b86a1

hschabau authored Apr 09, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6306 95c5a404-1f88-0410-a6b0-c3f062b6f34a

562b86a1

update · 3ff0b352

hschabau authored Apr 09, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6305 95c5a404-1f88-0410-a6b0-c3f062b6f34a

3ff0b352

Fixed race condition if MSA file malformed · 80e9112e

mvalle authored Apr 09, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@6304 95c5a404-1f88-0410-a6b0-c3f062b6f34a

80e9112e

22 Feb, 2013 1 commit

Removed dead test code · 9e38f089

mvalle authored Feb 22, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5975 95c5a404-1f88-0410-a6b0-c3f062b6f34a

9e38f089

20 Feb, 2013 1 commit

Added hyp selection also for MPI jobs · a8f4ae3e

mvalle authored Feb 20, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5956 95c5a404-1f88-0410-a6b0-c3f062b6f34a

a8f4ae3e

14 Feb, 2013 2 commits

added first FastCodeML spec file for Vital-IT RPM generation · 5bc80a74

hstockin authored Feb 14, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5927 95c5a404-1f88-0410-a6b0-c3f062b6f34a

5bc80a74

Added immediate check on the optimizer code. · 363e5706

mvalle authored Feb 14, 2013

Corrected help line for the -m option
For the global optimizer set the timeout to 24 hours

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5926 95c5a404-1f88-0410-a6b0-c3f062b6f34a

363e5706

07 Feb, 2013 3 commits

Fixed doxyfile with the new cpv scaling · c96c93c7

mvalle authored Feb 07, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5891 95c5a404-1f88-0410-a6b0-c3f062b6f34a

c96c93c7

Fixed cpv scalind for new likelihood · 4e5b7063

mvalle authored Feb 07, 2013

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5890 95c5a404-1f88-0410-a6b0-c3f062b6f34a

4e5b7063

Implemented CPV scaling · 74cadc80

mvalle authored Feb 07, 2013

Rationalized include files
Fixed CMakeLists for MPI on eiger


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5881 95c5a404-1f88-0410-a6b0-c3f062b6f34a

74cadc80

05 Feb, 2013 2 commits

Removed global scaling code · 53d56791

mvalle authored Feb 05, 2013

Started adding code for CPV scaling to avoid under/overflow
Added new option in CMake to enable local scaling

git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5867 95c5a404-1f88-0410-a6b0-c3f062b6f34a

53d56791

Added guard against infinites in results · 22133b10

mvalle authored Feb 05, 2013

Added print of no pre stop switch
Fixed global scaling code


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5861 95c5a404-1f88-0410-a6b0-c3f062b6f34a

22133b10

01 Feb, 2013 1 commit

Different seed for different MPI processes. · 177d77f5

mvalle authored Feb 01, 2013

Minor code cleaning.
Minor message from exception cleaning.


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5842 95c5a404-1f88-0410-a6b0-c3f062b6f34a

177d77f5

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 2 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