###  README --- pmodeltest/

## Copyright 2011 Francois Serra
##
## Keywords: Phylogeny modeltest model selection AIC Akaike

Tests evolutionary models like jModelTest but also for proteins.
'bitfast' option allows to run topology optimization on most weighted models.
Return 'best' tree with SH branch support value.

All based on the behavior of jModelTest:
 jModelTest: phylogenetic model averaging.
 Posada D
 Mol Biol Evol25p1253-6(2008 Jul)

and ProtTest:
 ProtTest: selection of best-fit models of protein evolution.
 Abascal F, Zardoya R, Posada D
 Bioinformatics21p2104-5(2005 May 1)

WARNING: use phyml version: 20110919
         available at: http://code.google.com/p/phyml/


BEFORE ALL, test:
python test_all.py


Usage:
python pmodeltest.py -i example/protein.phy [-o tree] [-O trees] [running options]