NAME
pllprac - Programming Practical of the Exelicis Lab using the Phylogenetic Likelihood Library (PLL).

SYNOPSIS
pllprac [-a|b] [-e|m] [-v] phylip_file

DESCRIPTION
This program takes a phylip multiple sequence alignment file as input and evaluates all possible 203 time-reversible substitution matrices on this data. It then takes the best matrix as the substitution model to run a full ML tree search for the taxa in the file. The resulting tree is outputted to a file.

OPTIONS

• -a|b: Use the (A)IC or (B)IC as criterion for the model. Default is BIC.
• -e|m: Use (E)mpirical base frequencies or (M)L estimates. Default is ML.
• -v: Verbose user output.

ENVIRONMENT

• PLL: In order to run this program, you need an installation of the Phylogenetic Likelihood Library (PLL), which can be obtained from http://www.libpll.org/
• MPI: The program can be compiled with MPI support via make mpi.

AUTHOR
Lucas Czech [email protected]