Phylogenomic analysis software tools and databases

Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection and the demographic changes and migration patterns of species. The advancement of sequencing technologies has taken…

Phylogenomics steps

Phylogenomic analysis software tools and databases

Most Recent Tools

PLCT
Desktop

PLCT Partially Labeled Coalescent Tree

Allows to determine reconciliation feasibility. PLCT aims to encode the set of…

Allows to determine reconciliation feasibility. PLCT aims to encode the set of species-specific loci that must be orthologous. It captures the constraints implied by the multiple loci and multiple…

bayou
Desktop

bayou

Permits to study adaptive evolution using multi-optima Ornstein-Uhlenbeck (OU)…

Permits to study adaptive evolution using multi-optima Ornstein-Uhlenbeck (OU) models. bayou incorporates different methods into a flexible software package for the R statistical environment. It also…

STS
Desktop

STS Sequential Tree Sampler

Implements several different transition kernels for updating a phylogenetic…

Implements several different transition kernels for updating a phylogenetic posterior with new sequences. STS is an open source package that updates an other distribution generated by MrBayes with…

ClonalOrigin
Desktop

ClonalOrigin

Allows to work about the history of recombination events that affected a given…

Allows to work about the history of recombination events that affected a given sample of bacterial genomes. ClonalOrigin run on as comparative analysis of sequences of a sample of bacterial genomes…

Most Popular Tools

EvolView
Web

EvolView

A comprehensive web application for visualizing, annotating and managing…

A comprehensive web application for visualizing, annotating and managing phylogenetic trees. Evolview allows users to visualize phylogenetic trees in various formats, customize the trees through…

PhyloPat
Dataset

PhyloPat

Allows the complete Ensembl gene database to be queried using phylogenetic…

Allows the complete Ensembl gene database to be queried using phylogenetic patterns. PhyloPat offers the possibility of querying with binary phylogenetic patterns or regular expressions, or through a…

GapAdj
Desktop

GapAdj Gapped Adjacencies

A synteny-based method that is flexible enough to handle a model of evolution…

A synteny-based method that is flexible enough to handle a model of evolution involving whole genome duplication events, in addition to rearrangements, gene insertions, and losses. Ancestral…

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