mlin/PhyloCSF

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|                 http://compbio.mit.edu/PhyloCSF                     | 
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SOURCE DISTRIBUTION

Compiling PhyloCSF from source may be difficult for most users,
because it requires an Objective Caml toolchain that's probably not
already present on your system. For this reason, we provide
precompiled binaries for Linux and Mac OS X on our website.

DEPENDENCIES

- GNU Scientific Library 
* Objective Caml 3.11+, with native code compiler
* findlib
* OCaml Batteries Included 1.20+
* ocamlgsl 0.60+
- ocaml+twt 0.92+ http://people.csail.mit.edu/mikelin/ocaml+twt/

* These can be set up using GODI: http://godi.camlcity.org/

The 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.

COMPILING

Assuming the above dependencies are satisfied:
1. pushd CamlPaml; make install; popd
2. pushd PhyloCSF; make; popd
3. PhyloCSF/_build/PhyloCSF.native is the executable and can be used
   with the parameters in PhyloCSF_Parameters/