The study of discrete characters is crucial for the understanding of evolutionary processes. Even though great advances have been made in the analysis of nucleotide sequences, computer programs for non-DNA discrete characters are often dedicated to specific analyses and lack…
Desktop app
SimPhy SimPhy

SimPhy

A software package for the simulation of multiple gene families evolving under…

A software package for the simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer –all three potentially leading to…

Desktop app
BadiRate BadiRate

BadiRate

A software tool to estimate family turnover rates, as well as the number of…

A software tool to estimate family turnover rates, as well as the number of elements in internal phylogenetic nodes, by likelihood-based methods and parsimony. BadiRate implements two stochastic…

Desktop app
BayesTraits BayesTraits

BayesTraits

A computer package for performing analyses of trait evolution among groups of…

A computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available, these can be created using BayesPhylogenies.…

Desktop app
Bayesian Estimation… Bayesian Estimation for Gene Family Evolution

BEGFE Bayesian Estimation for Gene Family Evolution

A Bayesian method for estimating the evolutionary history of gene families.…

A Bayesian method for estimating the evolutionary history of gene families. BEGFE implements a Markov Chain Monte Carlo algorithm to estimate the posterior probability distribution of the birth and…

Desktop app
Computational… Computational Analysis of gene Family Evolution

CAFE Computational Analysis of gene Family Evolution

Enables the accurate estimation of rates of gene family evolution when there…

Enables the accurate estimation of rates of gene family evolution when there are errors in the observed gene family sizes. By allowing users to marginalize over the uncertainty in the observed gene…

Desktop app
Count Count

Count

A software package for the analysis of numerical profiles on a phylogeny. It is…

A software package for the analysis of numerical profiles on a phylogeny. It is primarily designed to deal with profiles derived from the phyletic distribution of homologous gene families, but is…

Web app
DupliPHY DupliPHY

DupliPHY

A software tool to determine the evolutionary histories of gene families over a…

A software tool to determine the evolutionary histories of gene families over a phylogenetic tree. Given a set of gene family sizes and a phylogenetic tree DupliPHY will calculate the ancestral…

Desktop app
Web app
DupliPHY-ML DupliPHY-ML

DupliPHY-ML

DupliPHY is a software tool to determine the evolutionary histories of gene…

DupliPHY is a software tool to determine the evolutionary histories of gene families using maximum likelihood. Given a set of gene family sizes and a phylogenetic tree DupliPHY-ML will calculate the…

Desktop app
DiscML DiscML

DiscML

Performs maximum likelihood estimation for evolutionary rates of discrete…

Performs maximum likelihood estimation for evolutionary rates of discrete characters on a provided phylogeny with the options that correct for unobservable data, rate variations, and unknown prior…

Desktop app
Web app
Gain and Loss Mapping… Gain and Loss Mapping Engine

GLOOME Gain and Loss Mapping Engine

A user-friendly web server that accurately infers branch-specific and…

A user-friendly web server that accurately infers branch-specific and site-specific gain and loss events. The novel inference methodology is based on a stochastic mapping approach utilizing models…

Desktop app
markophylo markophylo

markophylo

Allows for fitting of maximum likelihood models using Markov chains on…

Allows for fitting of maximum likelihood models using Markov chains on phylogenetic trees for analysis of discrete character data. Examples of such discrete character data include restriction sites,…

Desktop app
Mesquite Mesquite

Mesquite

A modular, extendible software tool for evolutionary biology, designed to help…

A modular, extendible software tool for evolutionary biology, designed to help biologists organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of…

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