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Showing 4 records out of 4 total

Categories: Evolutionary biology - Software type(s): website - tool
The Coev-Web platform is a user-friendly interface of the command-line program Coev. The platform allows the evaluation of coevolving positions and their evolutionary profile based on the aligned sequences and a phylogenetic tree. It can also simulate coevolving pairs of positions along a given phylogenetic tree.
Categories: Evolutionary biology, Population genetics - Software type(s): CLI - tool
Continuous time conjunctive Bayesian networks (ct-cbn) are a family of graphical models describing the accumulation of mutations under order constraints. The software allows for the estimation of the network from cross-sectional data, such as mutation profiles of cancer or HIV patients.
keywords: Bayesian network
Categories: proteomics, (Protein modifications), Genomics, (characterisation/annotation), Systems biology, Transcriptomics - Software type(s): website, GUI - tool
MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets.
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.