Bug#876356: ITP: clonalframeml -- Efficient Inference of Recombination in Whole Bacterial Genomes
Package: wnpp
Severity: wishlist
Owner: Andreas Tille <tille@debian.org>
* Package name : clonalframeml
Version : 1.11
Upstream Author : Xavier Didelot <xavier.didelot@gmail.com>
* URL : https://github.com/xavierdidelot/ClonalFrameML
* License : GPL, LGPL
Programming Lang: C++
Description : Efficient Inference of Recombination in Whole Bacterial Genomes
ClonalFrameML is a software package that performs efficient inference of
recombination in bacterial genomes. ClonalFrameML was created by Xavier
Didelot and Daniel Wilson. ClonalFrameML can be applied to any type of
aligned sequence data, but is especially aimed at analysis of whole
genome sequences. It is able to compare hundreds of whole genomes in a
matter of hours on a standard Desktop computer. There are three main
outputs from a run of ClonalFrameML: a phylogeny with branch lengths
corrected to account for recombination, an estimation of the key
parameters of the recombination process, and a genomic map of where
recombination took place for each branch of the phylogeny.
.
ClonalFrameML is a maximum likelihood implementation of the Bayesian
software ClonalFrame which was previously described by Didelot and
Falush (2007). The recombination model underpinning ClonalFrameML is
exactly the same as for ClonalFrame, but this new implementation is a
lot faster, is able to deal with much larger genomic dataset, and does
not suffer from MCMC convergence issues
Remark: This program is packaged since it is to some extend a successor
of clonalframe which might be lost due to the removal of Qt4. It will
be maintained by the Debian Med team at
https://anonscm.debian.org/git/debian-med/clonalframeml.git
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