wardwheeler / poy5

Phylogenetic analysis program for general data inclusing unaligned sequence data

POY5

Phylogenetic analysis program for general data inclusing unaligned sequence data Instruction to compile poy5.1.2a Ward Wheeler Sept. 4, 2018

Citation: Wheeler, W. C., N. Lucaroni, L. Hong, L. M. Crowley, and A. Varón. 2015. POY version 5: Phylogenetic analysis using dynamic homologies under multiple optimality criteria. Cladistics 31:189-196.

Due to OCAML compiler changes only Ocaml 4.01.0 will work properly

Additional packages required: (for Ubuntu 18.04) sudo apt-get install lapack sudo apt-get install gfortran sudo apt-get install mpi (if you want parallel execution via MPI) sudo apt-get install zlib1gcd -dev

To compile with OCaml 4.01.0:

install POY package in PATH navigate to PATH/src make clean

./configure --enable-large-alphabets --enable-long-sequences --enable-unsafe --enable-likelihood --enable-interface=flat

for parallel add --enable-mpi CC=mpicc

ocamlbuild poy.native

binary in ./_build/poy.native