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Bug#807486: ITP: INDELible -- A powerful and flexible simulator of biological evolution

Package: wnpp
Severity: wishlist
Owner: "Debian Med Team" <debian-med@lists.debian.org>

* Package name    : INDELible
  Version         : 1.03
  Upstream Author : William Fletcher
* URL             : http://abacus.gene.ucl.ac.uk/software/indelible/
* License         : GPL
  Programming Lang: C++
  Description     : A powerful and flexible simulator of biological evolution

INDELible is a new, portable, and flexible application for biological
sequence simulation that combines many features in the same place for
the first time. Using a length-dependent model of indel formation it
can simulate evolution of multi-partitioned nucleotide, amino-acid,
or codon data sets through the processes of insertion, deletion, and
substitution in continuous time.
Nucleotide simulations may use the general unrestricted model or the
general time reversible model and its derivatives, and amino-acid
simulations can be conducted using fifteen different empirical rate
matrices. Substitution rate heterogeneity can be modelled via the
continuous and discrete gamma distributions, with or without a proportion
of invariant sites. INDELible can also simulate under non-homogenous
and non-stationary conditions where evolutionary models are permitted
to change across a phylogeny.
Unique among indel simulation programs, INDELible offers the ability to
simulate using codon models that exhibit nonsynonymous/synonymous rate
ratio heterogeneity among sites and/or lineages.

This package will be maintained as part of the Debian Med packaging team.

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