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Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions
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Latest commit 97a4324 Jan 13, 2016 @iljungr 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).
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PhyloCSF_Examples
PhyloCSF_Parameters
lib/CamlPaml
src
.gitignore
.travis-ci.sh
.travis.yml
LICENSE
Makefile
PhyloCSF
README

README

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SOURCE DISTRIBUTION

Please see our web site for more information about PhyloCSF and how to use it.
PhyloCSF is written in OCaml. This source distribution is divided into a
library, CamlPaml, containing generic infrastructure for phylogenetic rate
models, and a program implementing the PhyloCSF-specific models and driver
program. With additional development, the CamlPaml library will eventually be
released as a separate entity, but for now it is just part of this
distribution.

Here are the steps to build the source:

[1] Install the OCaml package manager OPAM

http://opam.ocamlpro.com/doc/Quick_Install.html

This will install a minimal OCaml toolchain (if not already present on your
system) and the OPAM package manager. Once it's installed, initialize your
shell environment by running: eval $(opam config env)

[2] Install dependencies using OPAM

opam install batteries ocaml+twt gsl

The gsl package may require you to separately install the GNU Scientific
Library (GSL) from: http://www.gnu.org/software/gsl/
On Debian/Ubuntu systems GSL is available in the 'libgsl0-dev' package, and on
Mac OS X, 'gsl' is available in both Homebrew and MacPorts.

[3] Compile PhyloCSF

Now just run 'make' in this directory. This will build and install the
CamlPaml library, then compile the PhyloCSF executable and copy it to
this directory. You can then use the ./PhyloCSF dispatch script like the
examples found on our website, e.g.

./PhyloCSF 12flies PhyloCSF_Examples/tal-AA.fa

PhyloCSF should be usable in this way by anyone on the machine/cluster with rx
permissions; they don't have to set up OPAM or anything else. PhyloCSF can
be started from any working directory.

If you want to 'install' PhyloCSF somewhere, you must transplant PhyloCSF,
PhyloCSF.ARCH (where e.g. ARCH=Linux.x86_64), and the PhyloCSF_Parameters
directory to the desired location.
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