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Model selection software tools | Phylogenomics

Molecular phylogenetics is a powerful tool for inferring both the process and pattern of evolution from genomic sequence data. Statistical approaches, such as maximum likelihood and Bayesian inference, are now established as the preferred methods of inference. The choice of models that a researcher uses for inference is of critical importance, and there are established methods for model selection conditioned on a particular type of data, such as nucleotides, amino acids, or codons. Source text: Whelan et al., 2015.

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A bioinformatic tool for the selection of best-fit models of amino acid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike information criterion (AIC), Bayesian information criterion (BIC) score or decision theory criterion (DT). At the same time, ProtTest obtains model-averaged estimates of different parameters (including a model-averaged phylogenetic tree) and calculates their importance. ProtTest 3 can be executed in parallel in HPC environments as: (i) a GUI-based desktop version that uses multicore processors; (ii) a cluster-based version that distributes the computational load among nodes; and (iii) as a hybrid multicore cluster version that achieves speed through the distribution of tasks among nodes while taking advantage of multicore processors within nodes.
A Java library that lets users use text to quickly and efficiently define novel forms of discrete data and create new substitution models that describe how those data change on a phylogeny. GeLL allows users to define general substitution models and data structures in a way that is not possible in other existing libraries, including mixture models and non-reversible models. Classes are provided for calculating likelihoods, optimizing model parameters and branch lengths, ancestral reconstruction and sequence simulation.
SPIn / model Selection in Phylogenetics based on algebraic INvariants
Uses linear invariants defining the spaces of all phylogenetic mixtures under a given model. SPIn is a novel approach to select an evolutionary model in phylogenetics. This tool requires no input tree and is designed to deal with nonhomogeneous phylogenetic data consisting of multiple sequence alignments showing different patterns of evolution, for example, concatenated genes, exons, and/or introns. It successfully recovers the underlying evolutionary model and is shown to perform better than existing approaches.
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