/PhyloCSF

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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
Commits on Mar 21, 2012

  1. fix ocaml+twt submodule and update README with more detailed instruct… 

    …ions
    committed Mar 21, 2012
    ec014de
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

    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

  2. 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 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. added ocaml+twt as submodule

    committed Jan 27, 2011
    05a5b5e