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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.

A second story:

Castor and Pollux (or, in greek Polydeuces) were half twin brothers in the greek and latin mitology, and they were known together as Dioscuri. Castor was the mortal son of Tyndareous, while Pollux was the divine son of Zeus. They were regarded as helpers of humankind in time of difficulties or to win challenges. The separation between mortal and immortal nature of the two brothers could -- with some degree of immagination -- suggest a link between the two different steps of indel-aware phylogenetic inference, which requires that both sequence alignment and the phylogenetic tree inference interpret indels as evolutionary events and account for their contribution.


Documentation

You can find tutorial, examples and guides on our Wikipages


Licence

* 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
*
* Castor is distributed in the hope that it will be useful, but WITHOUT
* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
* FITNESS FOR A PARTICULAR PURPOSE.
*
* This software is based and extends the Bio++ libraries which are
* developed by the Bio++ Development Team <http://biopp.univ-montp2.fr>
*
* This software is governed by the CeCILL  license under French law and
* abiding by the rules of distribution of free software.  You can  use,
* modify and/ or redistribute the software under the terms of the CeCILL
* license as circulated by CEA, CNRS and INRIA at the following URL
* "http://www.cecill.info".
*
* As a counterpart to the access to the source code and  rights to copy,
* modify and redistribute granted by the license, users are provided only
* with a limited warranty  and the software's author,  the holder of the
* economic rights,  and the successive licensors  have only  limited
* liability.
*
* In this respect, the user's attention is drawn to the risks associated
* with loading,  using,  modifying and/or developing or reproducing the
* software by the user in light of its specific status of free software,
* that may mean  that it is complicated to manipulate,  and  that  also
* therefore means  that it is reserved for developers  and  experienced
* professionals having in-depth computer knowledge. Users are therefore
* encouraged to load and test the software's suitability as regards their
* requirements in conditions enabling the security of their systems and/or
* data to be ensured and,  more generally, to use and operate it in the
* same conditions as regards security.
*
* The fact that you are presently reading this means that you have had
* knowledge of the CeCILL license and that you accept its terms.

Support

In case of bugs or improvement suggestions feel free to: - File an issue using via our issue collector here - Write to Lorenzo Gatti - Write to Massimo Maiolo

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Latest update

Build on commit: refs/heads/develop a5c173949e465945497fecd02d8f3c0ceeeb5109

On date: 31 Jul 2018, 16:00:20