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PAML / Phylogenetic Analysis by Maximum Likelihood
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 the rich repertoire of evolutionary models implemented, which can be used to estimate parameters in models of sequence evolution and to test interesting biological hypotheses. Uses of the programs include estimation of synonymous and nonsynonymous rates (dN and dS) between two protein-coding DNA sequences, inference of positive Darwinian selection through phylogenetic comparison of protein-coding genes, reconstruction of ancestral genes and proteins for molecular restoration studies of extinct life forms, combined analysis of heterogeneous data sets from multiple gene loci, and estimation of species divergence times incorporating uncertainties in fossil calibrations.
BEAST / Bayesian Evolutionary Analysis by Sampling Trees
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 a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results. It uses an XML input format that allows the user to design and run a large range of models. We also include a program that can convert NEXUS files into this format.
DAMBE / Data Analysis for Molecular Biology and Evolution
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 the putative Dalgarno sequences (SDs) in all protein-coding sequences and outputs a variety of summary statistics to show which gene has a strong and optimally positioned SD/anti-SD (aSD). Moreover, it can indicate gene location in the output sequence file.
Physher
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 (strict clock model). Alternatively, rate variation among lineages can be taken into account using two different parameterisations: local and discrete clock. Using two empirical data sets we show that our discrete clock estimates are similar to those obtained by other methods, and that Physher outperformed some methods in the estimation of the root age of an influenza virus data set. A simulation analysis suggests that Physher can outperform a Bayesian method when the real topology contains two long branches below the root node, even when evolution is strongly clock-like.
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