likelihood-based morphological phylogenetics
The INSTALL file has the automake/autoconf boilerplate. The basics are:
$ autreconf # may fail on the first time
$ automake add-missing
$ autoreconf # should succeed
$ CC=/usr/bin/clang CXX=/usr/bin/clang++ ./configure --prefix=$PWD/installed --with-ncl=/tmpncl/install --enable-debugging=yes --enable-asserts
$ make
$ make check
The two arguments should be a data file (NEXUS by default) and a -m flag followed by the path to an INI-style configuration file:
$ ./src/mtree -mtests/jc.ini jc.nex
Will trigger a scoring of the tree in jc.nex with the data in that file using an Mk model.
The section and setting names of the INI file are case-sensitive. The values are only case-sensitive when they refer to filepaths.
The currently supported values (using section/setting as a concise way to indicate the section and setting name) are:
| Section/Setting | Values | Meaning |
|---|---|---|
| action/action | LScore | Likelihood score with no branch length or parameter optmization |
`action/action = LScore (score the tree with no branch length or parameter optimization)
Code written by Liam Heins and Mark T. Holder with many routines/ideas taken from: Nexus Class Library (by Paul Lewis) Phylogenetic Likelihood Library (by Flouris et at) PAML (by Ziheng Yang)
Test code uses bash functions by Mitch Frazier from http://www.linuxjournal.com/content/floating-point-math-bash INI file parsing code (ini.c, ini.h, INIReader.cpp, INIReader.cpp) is from the inih project https://code.google.com/p/inih/ which is released under the BSD License.
Thanks to the US National Science Foundation and the Heidelberg Institute for Theoretical Studies.