Package: wnpp Severity: wishlist Owner: "Debian Med Team" <debian-...@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.
