Castor - Indel-aware phylogenetic tree inference

Castor is a phylogenetic tree inference software that implements a new class of indel-aware substitution models in the Maximum Likelihood framework.

There are two stories about the origin of the name Castor. The first one:

Indels leaves traces of their presence on the alignment in the form of small (or big) stretches of gap characters (-), thus generating sequence alignments made of several unconnected segments. These marks resemble those left by beavers (lat. genus name Castor) on logs and trees, which they use to build dams and lodges. Since sequence alignment and tree inference are two interdipendent inference steps, we pictured our indel-aware (the nibbles) phylogeny inferring software as a beaver (Castor) nibbling at the (phylogenetic) trees in the attempt of building a damn.


You can find tutorial, examples and guides on our Wikipages


 * Castor is a computer program whose purpose is to infer phylogentic trees
 * under indel-aware and indel-non-aware substitution models for nucleotide,
 * protein, and codon datasets
 * This software is based and extends the following libraries:
 * - the Bio++ libraries
 *   developed by the Bio++ Development Team <>
 * - The Tree Search Heuristic Library (TSH-LIB)
 *   developed by L. Gatti & M. Maiolo <>
 * Castor is distributed in the hope that it will be useful, but WITHOUT
 * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
 * Castor is a free software: you can redistribute it and/or modify it
 * under the terms of the GNU Lesser General Public License as published
 * by the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * You should have received a copy of the GNU Lesser General Public
 * License along with Castor. If not, see <>.


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