Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent.
A hierarchical clustering method based on likelihood-ratio testing that identifies congruent loci for phylogenomic analysis. Concaterpillar also includes a test for shared relative evolutionary rates between genes indicating whether they should be analyzed separately or by concatenation. In simulation studies, the performance of this method is excellent when a multiple comparison correction is applied.
Explores the genomic tree space and detect outlier genes and species based on multiple co-inertia analysis (MCOA), which efficiently captures and compares the similarities in the phylogenetic topologies produced by individual genes. Phylo-MCOA allows the rapid identification of outlier genes and species by extracting the similarities and discrepancies, in terms of the pairwise distances, between all the species in all the trees, simultaneously. This is achieved by using MCOA, which finds successive decomposition axes from individual ordinations (i.e., derived from distance matrices) that maximize a covariance function.
Detects overrepresented clusters in a hierarchical tree. TreeTracker compares a hierarchical and a dichotomic non-hierarchical classification of elements, in order to find clusters in a hierarchical tree in which elements of a given "flat" partition are overrepresented.
A congruence method that accommodates both very large numbers of genes and high degrees of incongruence. Conclustador uses clustering algorithms to identify subsets of genes based on similarity of phylogenetic signal. It involves only a single phylogenetic analysis per gene, and therefore, computation time scales nearly linearly with the number of genes in the data set. We show that our method performs very well with sets of sequence alignments simulated under a wide variety of conditions.
An open source tool that can be used to discover horizontally transferred genes, recombining areas of chromosomes, and the phylogenetic 'core' of a genome. Though we use it in an evolutionary context, it is generalizable to any clustering problem. Users can write extensions to calculate any distance metric on the unit interval and use these distances to flock any type of data.
Evaluates phylogenetic model adequacy. PhyloMAD is a statistical method that aims to improve phylogenetic inferences trustworthiness. It provides multiple approaches for estimating general time reversible (GTR) nucleotide substitution models as well as models of amino acid substitution. The software can be run through either a graphic user interface or via command-line and provides modulable outputs according users’ needs.