/PhyloCSF

History for PhyloCSF/src
Commits on Jan 18, 2015

  1. modernize ocamlbuild commands (3.12+)

    committed Jan 18, 2015
    c5cb773
Commits on Apr 15, 2014

  1. CamlPaml.PhyloLik.node_posterior: avoid unnecessary computation of al… 

    …l betas when computing posterior distribution for the root. This commit approximately doubles the speed of PhyloCSF, since it was calling node_posterior on the root to compute the ancestral composition score.
    committed Apr 15, 2014
    3b5bd0e
Commits on Apr 14, 2014

  1. Add simple fork-based parallelism for searching over frames/ORFs. 

    Depends on ForkWork (opam install forkwork). To use, compile PhyloCSF
with ```make FORKWORK=1``` and run with ```-p <number of cores>```.
    committed Apr 13, 2014
    87b7df6

  2. Travis CI

    committed Apr 14, 2014
    b4af4fb
Commits on Apr 13, 2014

  1. a few systematic/reproducible tests

    committed Apr 13, 2014
    8369815

  2. rename PhyloCSFTest => testSim

    committed Apr 13, 2014
    59e8eda
Commits on Mar 19, 2013

  1. tweaks to build against batteries 2.x

    committed Mar 19, 2013
    1f58835
Commits on Dec 25, 2012

  1. fixup whitespace

    committed Dec 25, 2012
    5590d23

  2. Change over to gsl-ocaml

    committed Dec 25, 2012
    9d8fa1f
Commits on May 5, 2012

  1. fix --allScores (issues #7 and #8)

    committed May 5, 2012
    2ab5975
Commits on Jan 19, 2012
  1. @iljungr

    Tiny cleanup in PhyloCSFModel.ml. 

    To Do: There is no longer any warning when it can't find
   a good branch length parameter. It would be good to add something
   to diagnostics in llr_MaxLik to indicate this.
    iljungr committed Jan 19, 2012
    5e18fc5
  2. @iljungr

    Removed Out_of_range errors. Instead, use end of range as branch leng… 

    …th factor.
    iljungr committed Jan 19, 2012
    86ae3ff
Commits on Dec 25, 2011

  1. add ancestral sequence composition score

    Michael Lin committed Dec 25, 2011
    df362d5
Commits on Dec 24, 2011

  1. --orf FromLastStop and ToOrFromStop options

    Michael Lin committed Dec 24, 2011
    373300f
Commits on Feb 4, 2011

  1. still further regularization tweaks

    Michael Lin committed Feb 4, 2011
    a1c5c77

  2. further regularization adjustments

    committed Feb 4, 2011
    d9aba11

  3. adjust regularization again

    committed Feb 4, 2011
    5ad70ab
Commits on Jan 27, 2011

  1. Revert "eliminate regularization priors in omega test -- not really n… 

    …eeded on second thought" -- needed on third thought

This reverts commit e7ae86e.
    committed Jan 27, 2011
    0b656ac

  2. eliminate regularization priors in omega test -- not really needed on… 

    … second thought
    committed Jan 27, 2011
    e7ae86e

  3. omega test strategy optionally reads in assumed values of omega_H1 an… 

    …d sigma_H1 from parameter files
    committed Jan 27, 2011
    18ddbea

  4. additional option parser cleanup, including hiding of dangerous --all… 

    …owRefGaps option
    committed Jan 27, 2011
    f58909e

  5. add ability to report diagnostic information from parameter estimatio… 

    …n procedures
    committed Jan 27, 2011
    5182e9d

  6. Merge branch 'OmegaTest' 

    Conflicts:
	src/PhyloCSF.ml
    committed Jan 27, 2011
    3df28c9

  7. add diagnostic info for omega test, and fix some typos

    committed Jan 27, 2011
    ba40fa0

  8. option to report score of all ORFs evaluated, not just the max

    committed Jan 27, 2011
    c0df294

  9. further progress on omega test

    committed Jan 27, 2011
    3e0cf15
Commits on Jan 26, 2011

  1. first rough implementation of omega (dN/dS) test

    committed Jan 26, 2011
    294f6a5
Commits on Oct 25, 2010

  1. Merge branch 'master' of git@github.com:mlin/PhyloCSF

    Michael Lin committed Oct 25, 2010
    323aba4
Commits on Oct 18, 2010

  1. --orf=ATGStop adjustment -- to find start-to-stop ORFs only (not if i… 

    …t goes off the end of the alignment)
    committed Oct 18, 2010
    e57b7a0
Commits on Oct 16, 2010

  1. Merge branch 'master' of git@github.com:mlin/PhyloCSF

    Michael Lin committed Oct 16, 2010
    6ac9ffb

  2. branch length score (BLS) reporting

    committed Oct 16, 2010
    3f20052
Commits on Sep 30, 2010

  1. bugfix to --orf=ToFirstStop mode

    Michael Lin committed Sep 30, 2010
    3ead5b4
Commits on Sep 16, 2010

  1. detect whether parameter_set argument is a relative/absolute path

    Michael Lin committed Sep 16, 2010
    11ba130

  2. make executable find the parameters directory based on the PHYLOCSF_B… 

    …ASE env var
    Michael Lin committed Sep 16, 2010
    82967b1

  3. fix assertion failure with untranslatable sequences; add --orf=ToFirs… 

    …tStop
    Michael Lin committed Sep 16, 2010
    1cbdd48