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.
Offers a solution to choose among different models of nucleotide substitution. jModelTest includes five different model selection strategies, including hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC), and a performance-based decision theory method (DT). This tool assists users to monitor their jobs, displaying information about their current state and resources consumed.
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.
Selects optimal amino acid and nucleotide substitution models from Fasta or Phylip alignments. ModelGenerator supports 56 nucleotide and 96 amino acid substitution models. It uses the Akaike Information Criterion (AIC), the Bayesian Information Criterion (BIC) and hierarchical Likelihood-ratio tests (hLRTs) to select the best-fitting model of substitution. ModelGenerator uses the PAL library to perform its calculations and is part of the popular wEMBOSS package.
Provides a virtual portal that allows researchers to run multiple workflows. BioVel supplies a laboratory that gathers functionalities for supporting complex data biodiversity science and ecology research. It proposes workflow assortments in taxonomic refinement, ecological niche modeling, metagenomics, phylogenetics, population modeling, and ecosystem modeling which can be directly run or downloaded.
Designs for rapid phylogenetic model selection on protein coding genes. ModelOMatic is fast, with most families from PANDIT taking fewer than 150 s to complete, and should therefore be easily incorporated into existing phylogenetic pipelines.
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.