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| | ____ __ __ ___________ ______ | | |
| | / __ \/ /_ __ __/ /____ / ____/ ___// ____/ | | |
| | / /_/ / __ \/ / / / // __ \/ / \__ \/ /_ | | |
| | / ____/ / / / /_/ / // /_/ / /___ ___/ / __/ | | |
| | /_/ /_/ /_/\__, /_/ \____/\____//____/_/ | | |
| | /____/ | | |
| | | | |
| | http://compbio.mit.edu/PhyloCSF | | |
| +---------------------------------------------------------------------+ | |
| 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/ |