ParaPhylo Downloads

ParaPhylo and Source code
ParaPhylo with Proteinortho
Analyses and Results from the paper "Phylogenomics with Paralogs"

ParaPhylo is executed from the command line using:

java -jar ParaPhylo.jar -i <input file> -o <output file>
use —help for an overview on ParaPhylo‘s parameters

A tool for converting Proteinortho 5.x output into the ParaPhylo format is included and can be executed with the command:

java -jar ParaPhyloConverter.jar -p <proteinortho file> -g <proteinortho-graph file>

Note that IBM ILOG CPLEX Optimizer 12.6 is required for running ParaPhylo. Depending on your os and architecture, just copy the respective library, libcplex126.jinilib or cplex126.dll to ParaPhylo‘s subfolder “os/[linux|macosx|windows]/[x86|x86_64]”. The respective file is contained in the IBM ILOG CPLEX Optimizer 12.6 distribution.
Java 1.6 or later has to be installed on your system.

To run ParaPhylo with newer versions of IBM ILOG CPLEX Optimizer use ParaPhylo1271 for CPLEX version 12.7.1 or ParaPhylo1280 for the current CPLEX version 12.8.0.

Feel free to send bug reports or any other kind of impressions or suggestions on ParaPhylo to