ParaPhylo is a tool for reconstructing phylogenetic species trees based on information about paralogous genes. It relies on solving three intertwined NP-hard optimization problems: the cograph editing problem, the maximum consistent triple set problem, and the least resolved tree problem. Implemented as Integer Linear Program, paralogy-based phylogenies can be computed exactly for up to some twenty species and their complete protein complements.

ParaPhylo relies on the IBM ILOG CPLEX Optimizer 12.6. for which an academic license can be obtained for free.

ParaPhylo Downloads

Download ParaPhylo
Download 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

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ParaPhylo Publications

Reference for ParaPhylo:

M. Hellmuth, N. Wieseke, M. Lechner, H-P Lenhof, M. Middendorf, and P.F. Stadler
Phylogenetics from Paralogs
preliminary version of “Phylogenomics with Paralogs”
Workprint and Supplement

M. Hellmuth, N. Wieseke, M. Lechner, H-P Lenhof, M. Middendorf, and P.F. Stadler
Phylogenomics with Paralogs
Proceedings of the National Academy of Sciences (PNAS), 112(7):2058–2063, 2015
Workprint and Supplement