utcs Phylogenetics
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This webpage contains software developed by the UTCS Phylogenetics group, some in collaboration with others. Most of these methods are freely available in open source form, and licensed under (various) open source licenses. Please check carefully before using the code in your own software, since you may inherit the open source requirements of the source code.

SATé

  • software for simultaneous alignment and tree estimation

PASTA

  • the modern version of SATé, providing greater scalability and accuracy

DACTAL

  • software for computing very large trees without an input multiple sequence alignment

SuperFine

  • software for computing supertrees

SEPP

  • software for phylogenetic placement

GRAPPA

  • an open source software package for reconstructing phylogenies from gene order data

Rec-I-DCM3

  • a divide-and-conquer booster for large-scale phylogeny reconstruction

spruce

  • a Python package designed for simple supertree analysis

FastSP

  • a fast and memory-efficient Java application for comparing two multiple sequence alignments

DynaDup

  • a Dynamic Programing based Java application for building species trees from gene trees minimizing gene duplication and gene duplication and loss.

ratchet.pl

  • Perl script for running an MP Ratchet analysis in PAUP*
  • Created by Olaf R. P. Bininda-Emonds and modified by Tiffani L. Williams

BeeTLe

  • BeeTLe (version May 17, 2013).
  • From: K. Liu and T. Warnow, "Treelength Optimization for Phylogeny Estimation," PLoS ONE, vol. 7, no. 3:e33104, 2012, doi: 10.1371/journal.pone.0033104.

DCM-boosting

  • Disk Covering Methods for phylogenomic analyses.
  • From: Md. Shamsuzzoha Bayzid, Tyler Hunt and Tandy Warnow, "Disck Covering Methods Improve Phylogenomic Analyses", BMC Genomics (to appear).

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