Search Results for "phylogenetic"

set of classes used to handle input/outputs of bioinformatics data files and basic operations as multiple alignment and phylogenetic reconstruction.

Phylogenetic software that implements the algorithms "Fast Computation of Distance Estimators" and "Fast Neighbor Joining".

A number of software packages are available to generate DNA MSAs evolved under continuous-time Markov processes on phylogenetic trees. On the other hand, methods of simulating the DNA MSA directly from the transition matrices do not exist. Moreover, existing software restricts to the time-reversible models and it is not optimized to generate nonhomogeneous data (i.e. placing distinct substitution rates at different lineages). GenNon-H is the first package designed to generate multiple sequence alignments under the discrete-time Markov processes on phylogenetic trees, which samples directly from the transition matrices. ...

The Nexus Class Library (NCL) is a C++ library for interpreting data files created according to the NEXUS file format used in phylogenetic systematics and molecular evolution.

ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm.

This is a wxWidgets-based, cross-platform graphical frontend for the maximum-likelihood phylogenetic inference program RAxML created by Alexis Stamatakis (A. Stamatakis, Bioinformatics 22(21):2688-2690, 2006)

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

A python/C++ framework for Bayesian phylogenetic analysis.

PhyloCpp is (will be...) a C++ toolkit designed for the reading, writing and manipulation of phylogenetic trees with an emphasis on comparative methods, ancestral state reconstruction and characterization of the evolutionary process.

TreeSoft is a collection of softwares that build or manipulate phylogenetic trees.

DNA, Amino Acid And RNA Tests: free software for probabilistic measurement and annotation of biological sequences, using phylogenetic Markov chains and stochastic grammars.