/PhyloCSF

History for PhyloCSF/lib/CamlPaml
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. CamlPaml: add test coverage of codepaths for non-reversible rate matr… 

    …ices
    committed Apr 14, 2014
    874b617
Commits on Apr 13, 2014

  1. CamlPaml performance optimization: detect when Q is reversible and av… 

    …oid unnecessary use of complex numerics
    committed Jul 23, 2013
    8725d81
Commits on Aug 19, 2013

  1. CamlPaml.PhyloModel.P14n.update: simplify 'inheritance' of root prior… 

    … distribution for reversible models
    committed Aug 19, 2013
    fd3a0fb
Commits on Dec 25, 2012

  1. Change over to gsl-ocaml

    committed Dec 25, 2012
    9d8fa1f
Commits on Jan 21, 2012
  1. @iljungr

    Initialize random number generator in find_init to make results repro… 

    …ducible.
    iljungr committed Jan 21, 2012
    829d1b1
Commits on Jan 19, 2012
  1. @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 24, 2011

  1. lib/CamlPaml/PhyloModel: simulate from a specified root character

    Michael Lin committed Dec 24, 2011
    fb11f12
Commits on Feb 23, 2011

  1. CamlPaml.PhyloModel.P14n.instantiate_qs error check

    Michael Lin committed Feb 23, 2011
    ec951eb
Commits on Feb 7, 2011

  1. CamlPaml: PhyloModel.P14n checks variable domains; correction to Fit.… 

    …maximizer documentation
    Michael Lin committed Feb 7, 2011
    bafc397
Commits on Oct 26, 2010

  1. CamlPaml.Q.Diag.to_Pt_gc

    committed Oct 26, 2010
    0f01823

  2. CamlPaml.PhyloEM: a bit of cleanup

    committed Oct 26, 2010
    2b02c62

  3. CamlPaml.PhyloEM.d_ell_dQ_dxi bugfix

    committed Oct 26, 2010
    edcfbdd
Commits on Oct 25, 2010

  1. CamlPaml.T.congruent: correct assert statements

    Michael Lin committed Oct 25, 2010
    7bfbbe4
Commits on Sep 7, 2010

  1. CamlPaml: build adjustments for OCaml 3.11 compatibility

    Mike Lin committed Sep 7, 2010
    5b938c8

  2. CamlPaml: new tests based on examples from BEAGLE

    committed Sep 7, 2010
    eaa9658
Commits on Sep 6, 2010

  1. rename CamlPaml.Infer -> CamlPaml.PhyloLik

    committed Sep 6, 2010
    6bb5eda
Commits on Sep 3, 2010

  1. reorganize directories and clean up build infrastructure

    committed Sep 3, 2010
    b12e634