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Molecular dating software tools | Phylogenomics

Molecular dating of phylogenetic trees is a growing discipline using sequence data to co-estimate the timing of evolutionary events and rates of molecular evolution. All molecular-dating methods require converting genetic divergence between…
PAML
Desktop

PAML Phylogenetic Analysis by Maximum Likelihood

A package of programs for phylogenetic analyses of DNA and protein sequences…

A package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood (ML). PAML may be used to compare and test phylogenetic trees, but their main strengths lie in…

BEAST
Desktop

BEAST Bayesian Evolutionary Analysis by Sampling Trees

A cross-platform program for Bayesian phylogenetic analysis of molecular…

A cross-platform program for Bayesian phylogenetic analysis of molecular sequences. BEAST estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as…

Physher
Desktop

Physher

A maximum likelihood-based method for estimating evolutionary rates and…

A maximum likelihood-based method for estimating evolutionary rates and divergence times from genetic data. The simplest model assumes that the substitution rate is constant over the whole phylogeny…

TipDate
Web

TipDate

Uses sequences that have been isolated at different dates to estimate their…

Uses sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate of the rate and also the associated date of…

DAMBE
Desktop

DAMBE Data Analysis for Molecular Biology and Evolution

Allows sequence manipulation and analysis in molecular biology, phylogenetics…

Allows sequence manipulation and analysis in molecular biology, phylogenetics and evolution. DAMBE is a software that can extract the sequence upstream of each coding sequences (CDSs). It identifies…

r8s
Desktop

r8s

Uses parametric, nonparametric and semiparametric methods to relax the…

Uses parametric, nonparametric and semiparametric methods to relax the assumption of constant rates of evolution to obtain better estimates of rates and times. r8s permits users to convert results to…

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