ALPHA: A Toolkit for Automated Local Phylogenomic Analyses
...thon-based application that provides an intuitive user interface for phylogenetic analyses and data visualizati...n. It has four distinct modes that are useful for different types of phylogenetic analysis: RAxML, File Convert...2235 days ago
DendroPy: a Python library for phylogenetic computing
...ndroPy is a Python library for phylogenetic computing. It provides classe...rocessing, and manipulation of phylogenetic trees and character matrices,...rts the reading and writing of phylogenetic data in a range of formats, s...n as a stand-alone library for phylogenetics, a component of more complex...2203 days ago
Ranbow: a haplotype assembler for polyploid genomes
...n: ranbow hap: for haplotyping ranbow eval: for evaluating of the assemble haplotypes by gold standard (long) reads ranbow phylo: for the phylogenetic analysis2164 days ago
Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment
Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements th...2163 days ago
MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the&...2163 days ago
2173 days ago
IQ-TREE: Efficient software for phylogenomic inference
A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar...1902 days ago
Retrieving Taxonomic Information with R
...rmation retrieval. Specifically, the taxonomy() function implemented in myTAI can be used to classify genomes according to phylogenetic classification into Phylostra...1710 days ago
1620 days ago
phyloXML: XML for evolutionary biology and comparative genomics
phyloXML (example) is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, suc...1608 days ago