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Showing 3 records out of 3 total
Arlequin [Computational and Molecular Population Genetics (L. Excoffier)]
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Categories: population genetics - Software type(s): CLI, GUI - tool
Arlequin provides the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. The graphical interface is designed to allow users to rapidly select the different analyses they want to perform on their data. One can explore the data, and analyze several times the same data set from different perspectives, with different selected options.
keywords: coalescent, computer package, distance, evolution, genetic data analysis, genomics, graphics, haplotype inference, model of evolution, population genetics, R, RFLP, selection, SNP
MLtree [Computational Phylogenetics (N. Salamin)]
[download] UP
Categories: phylogeny/evolution - Software type(s): CLI - tool
MLtree is a software to compute maximum likelihood optimization of models of character evolution (either DNA or phenotypic ones) along the branches of a phylogenetic tree. It is assuming that the phylogenetic tree is known.
keywords: character evolution, maximum likelihood, model of evolution
Phylogibbs [Genome Systems Biology (E. van Nimwegen)]
UP
Categories: genomics, (sequence alignment, similarity search), systems biology - Software type(s): website, CLI, GUI - tool
Phylogibbs is an algorithm for discovering regulatory sites in a collection of DNA sequences, including multiple alignments of orthologous sequences from related organisms.The algorithm uses a Gibbs sampling strategy, takes the phylogenetic relationships of the input sequences rigorously into account, and assigns realistic posterior probabilities to reported sites using a novel annealing+tracking strategy.
keywords: alignment, alignment analysis, animal, arthropod, Bayesian network, binding sites prediction, C, ChIP-seq, evolution, fungi, genetic data analysis, genomics, Gibbs sampler, HMM, human, insect, interaction, maximum likelihood, model of evolution, multiple sequence alignment (MSA), network, NGS, phylogibbs, population genetics, regulatory site, selection, sequence analysis, sequence comparison, short sequence alignment, similarity search, transcription factor binding site, transcription module, transcription regulation, transcriptome analysis, vertebrate