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Commits on Oct 16, 2023

• Added tree image for 120mammals.

  iljungr

  authored
  3d29221

• Added parameters for 120mammals

  iljungr

  committed
  bfa24ff

Commits on Feb 8, 2023

• Added Psi directory with coefficients for computing PhyloCSF-Psi.

  iljungr

  committed
  75eaac0

• Added 30mammals_mm39 and 35vertebrates_mm39

  iljungr

  committed
  305d888

Commits on Sep 13, 2019

• Added 53birds parameters

  iljungr

  committed
  6a26e7f

Commits on Aug 28, 2017

• Removed 8worms and all rn6 parameters because they are redundant.

  iljungr

  committed
  eda6eb8

• Added parameter sets 13mammals_rn6, 20vertebrates_rn6, 8worms, 26worms.

  iljungr

  committed
  029fc3f

Commits on Oct 3, 2016

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

  iljungr

  committed
  193e581

Commits on Jan 13, 2016

• 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: Sta…

  iljungr

  committed
  97a4324

Commits on Jan 18, 2015

• modernize ocamlbuild commands (3.12+)

  mlin

  committed
  c5cb773

Commits on Aug 28, 2014

• Added parameters for 21mosquitoes and 7yeast.

  iljungr

  committed
  e8378da

Commits on Apr 15, 2014

• CamlPaml.PhyloLik.node_posterior: avoid unnecessary computation of all betas when computing posterior distribution for the root. This commit approximately doubles the speed of PhyloCSF, since it wa…

  mlin

  committed
  3b5bd0e

Commits on Apr 14, 2014

• CamlPaml: add test coverage of codepaths for non-reversible rate matrices

  mlin

  committed
  874b617

• Use parallelism for the long Travis CI build.

  mlin

  committed
  dcd0fdf

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

  mlin

  committed
  87b7df6

• Travis CI

  mlin

  committed
  b4af4fb

Commits on Apr 13, 2014

• a few systematic/reproducible tests

  mlin

  committed
  8369815

• rename PhyloCSFTest => testSim

  mlin

  committed
  59e8eda

• CamlPaml performance optimization: detect when Q is reversible and avoid unnecessary use of complex numerics

  mlin

  committed
  8725d81

Commits on Aug 19, 2013

• CamlPaml.PhyloModel.P14n.update: simplify 'inheritance' of root prior distribution for reversible models

  mlin

  committed
  fd3a0fb

Commits on Apr 24, 2013

• Update README

  mlin

  committed
  01ab7bf

Commits on Mar 20, 2013

• Update README

  mlin

  committed
  9d77729

Commits on Mar 19, 2013

• Update README

  mlin

  committed
  88a7551

• Add dispatch script to set PHYLOCSF_BASE

  mlin

  committed
  0cfd7b8

• README with simplified build instructions

  mlin

  committed
  621ab98

• remove submodules and simplify Makefile

  mlin

  committed
  73b6739

• tweaks to build against batteries 2.x

  mlin

  committed
  1f58835

Commits on Dec 25, 2012

• fixup whitespace

  mlin

  committed
  5590d23

• Change over to gsl-ocaml

  mlin

  committed
  9d8fa1f

Commits on Oct 29, 2012

• Update Makefile to clean CDE

  mlin

  committed
  4a6fb44

• bump CDE submodule version

  mlin

  committed
  47611e1

Commits on Sep 23, 2012

• Makefile tweak

  mlin

  committed
  642d19f

Commits on Sep 22, 2012

• Makefile: tweak dependencies

  mlin

  committed
  96f9769

Commits on Aug 25, 2012

• additional build tweaks

  mlin

  committed
  5ebf405

Commits on Aug 24, 2012

• Makefile: build ocaml+twt automatically

  mlin

  committed
  93c8ce9

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