Software

3I - Internet-accessible Interactive Identification

ctap.inhs.uiuc.edu

Program to create internet-accessible interactive taxonomic keys.

363 visits Mar 24, 2024 Details

Component

taxonomy.zoology.gla.ac.uk

For analysis of phlyogenies. Includes a wide range of randomisation methods, consensus methods, tree comparison measures, and calculates reconciled trees. Now aging, and available …

251 visits Apr 21, 2025 Details

GeneTree

taxonomy.zoology.gla.ac.uk

Uses reconciled trees to compare gene trees and species trees, explaining incongruence between the phylogenies by postulating horizontal transfer, gene duplication and loss events.…

302 visits Sep 15, 2024 Details

MacClade

phylogeny.arizona.edu

A powerful Macintosh package for phylogenetic analysis. Not intended as a stand-alone tool to infer phylogeny, but excels in studying character evolution. Also provides tools for e…

136 visits Aug 10, 2025 Details

Mesquite

mesquiteproject.org

Experimental, modular software for evolutionary biology, designed to help biologists analyze comparative data about organisms.

486 visits Jul 18, 2024 Details

Nona - A Quick Guide to the Commands

gwu.edu

A brief overview of using Nona for phylogenetic analysis.

349 visits Sep 25, 2023 Details

PAML

abacus.gene.ucl.ac.uk

Phylogenetic analyses of DNA or protein sequences using maximum likelihood.

365 visits Nov 24, 2025 Details

PAUP*

paup.csit.fsu.edu

PAUP is the most widely used package for phylogenetic inference, and now implements maximum likelihood and distance methods as well as various forms of parsimony. Powerful and very…

460 visits May 24, 2024 Details

PHYLIP

evolution.genetics.washington.edu

Joe Felsenstein's suite of programs implementing perhaps the widest range of phylogenetic inference package. The most widely distributed phylogeny software. Includes distance, like…

348 visits Dec 24, 2025 Details

Phylo-Win

pbil.univ-lyon1.fr

Graphical color interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony, and maximum likelihood methods and bootstrap with any of them.

382 visits Jul 31, 2025 Details

Phylodendron

iubio.bio.indiana.edu

Java application for drawing phylogenetic trees. Allows you to save in various formats, print, edit, modify, and adorn the tree, and should work on any java runtime platform.

357 visits Apr 8, 2026 Details

RadCon

taxonomy.zoology.gla.ac.uk

A package implementing a wide range of consensus methods, including reduced consensus, and for calculation of MRP supertrees. Currently only available for Macs.

317 visits Sep 3, 2024 Details