/PhyloCSF

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Commits on Oct 3, 2016
  1. @iljungr

    Parameters for 100vertebrates (using 29mammal ECMs), 23flies, 49birds

    iljungr committed Oct 3, 2016
    193e581
Commits on Jan 13, 2016
  1. @iljungr

    Added parameters for 58mammals. Uses same matrices as 29 mammals but … 

    …tree for the 58 placental mammals subset of hg38.100way.commonNames.nh (two names were changed to remove special characters: Star-nosed_mole -> Star_nosed_mole; David's_myotis -> Davids_myotis).
    iljungr committed Jan 13, 2016
    97a4324
Commits on Jan 18, 2015

  1. modernize ocamlbuild commands (3.12+)

    committed Jan 18, 2015
    c5cb773
Commits on Aug 28, 2014
  1. @iljungr

    Added parameters for 21mosquitoes and 7yeast.

    iljungr committed Aug 28, 2014
    e8378da
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

  2. Use parallelism for the long Travis CI build.

    committed Apr 14, 2014
    dcd0fdf

  3. 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

  4. 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

  3. 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 Apr 24, 2013

  1. Update README

    committed Apr 24, 2013
    01ab7bf
Commits on Mar 20, 2013

  1. Update README

    committed Mar 20, 2013
    9d77729
Commits on Mar 19, 2013

  1. Update README

    committed Mar 19, 2013
    88a7551

  2. Add dispatch script to set PHYLOCSF_BASE

    committed Mar 19, 2013
    0cfd7b8

  3. README with simplified build instructions

    committed Mar 19, 2013
    621ab98

  4. remove submodules and simplify Makefile

    committed Mar 19, 2013
    73b6739

  5. 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 Oct 29, 2012

  1. Update Makefile to clean CDE

    committed Oct 29, 2012
    4a6fb44

  2. bump CDE submodule version

    committed Oct 29, 2012
    47611e1
Commits on Sep 23, 2012

  1. Makefile tweak

    committed Sep 23, 2012
    642d19f
Commits on Sep 22, 2012

  1. Makefile: tweak dependencies

    committed Sep 22, 2012
    96f9769
Commits on Aug 25, 2012

  1. additional build tweaks

    committed Aug 25, 2012
    5ebf405
Commits on Aug 24, 2012

  1. Makefile: build ocaml+twt automatically

    committed Aug 24, 2012
    93c8ce9
Commits on May 5, 2012

  1. Makefile minor tweaks

    committed May 5, 2012
    11c6c2a

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

    committed May 5, 2012
    2ab5975
Commits on Apr 30, 2012

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

    committed Apr 30, 2012
    2db5375

  2. README: fix OCAMLPATH

    committed Apr 30, 2012
    b634a29
Commits on Apr 12, 2012
  1. @iljungr

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

    iljungr committed Apr 12, 2012
    3b0bf5a
  2. @iljungr

    Added 20flies parameter files. (Matrices are copied from 12flies, and… 

    … tree

is from modENCODE.)
    iljungr committed Apr 12, 2012
    1f40ece
Commits on Mar 24, 2012

  1. Makefile section for building CDE package

    committed Mar 24, 2012
    70fe90f