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Commits on Jan 27, 2011

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

    committed Jan 27, 2011
    ba40fa0

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

    Michael Lin committed Oct 25, 2010
    323aba4

  2. CamlPaml.T.congruent: correct assert statements

    Michael Lin committed Oct 25, 2010
    7bfbbe4
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
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
Commits on Aug 31, 2010

  1. CamlPaml: build process cleanup

    committed Aug 31, 2010
    95d12fe

  2. performance improvement: --species

    committed Aug 31, 2010
    48a5bb0

  3. performance optimization: workspace reuse

    committed Aug 31, 2010
    2053832

  4. CamlPaml: stripped out intrinsic support for fixed-effect likelihood … 

    …models with multiple components, simplifying the interfaces
    committed Aug 31, 2010
    196aaa3
Commits on Aug 30, 2010

  1. documentation updates

    Michael Lin committed Aug 30, 2010
    5352b9a

  2. unit tests for CamlPaml.infer

    Michael Lin committed Aug 30, 2010
    ab59f92
Commits on Aug 27, 2010

  1. CamlPaml.PhyloModel.infer pass workspace through

    Michael Lin committed Aug 27, 2010
    9b80e45

  2. remove SSE2 stuff

    Michael Lin committed Aug 27, 2010
    be2731c

  3. rework of CamlPaml.Infer to use GSL matrices and BLAS

    Michael Lin committed Aug 27, 2010
    5c6ba27

  4. experimental version using SSE2 vectorization to speed up likelihood … 

    …calculations
    Michael Lin committed Aug 27, 2010
    ead4e66

  5. master makefile

    Michael Lin committed Aug 27, 2010
    b4d0efb

  6. minor bugfix to --orf=StopStop mode

    Michael Lin committed Aug 27, 2010
    0e5dd98
Commits on Aug 25, 2010

  1. small correction to README

    Michael Lin committed Aug 25, 2010
    6b986f6

  2. new options for input (gap handling) and output (DNA/AA sequences); A… 

    …ldh2 example
    Michael Lin committed Aug 25, 2010
    247096d
Commits on Aug 17, 2010

  1. require ungapped reference sequence; example alignments

    Michael Lin committed Aug 17, 2010
    1e2477d

  2. cleanup

    Michael Lin committed Aug 17, 2010
    11da727