Offers a unified framework for incorporating duplication/loss parsimony into phylogenetic tasks, including reconciling a gene tree with a species tree and estimating upper and lower bounds on the time of duplication; rooting an unrooted gene tree by minimizing duplication and loss events; rearranging a rooted gene tree in areas of weak sequence support to minimize the number of duplications and losses; resolving a non-binary gene tree by fitting it to a binary species tree.
A program for the analysis of how dependent phylogenies are related, by cophylogeny mapping. TreeMap performs cophylogeny mapping from a dependent evolutionary tree (e.g., a group of parasites) into an independent one (e.g., the hosts of those parasites), in order to recover the best possible coevolutionary explanation for the relationship between the two.
A package for accurate inference of coevolving characters as manifested by co-occurring gains and losses. CoPAP uses state-of-the-art probabilistic methodologies to infer coevolution and allows for advanced network analysis and visualization of phyletic data. The tool has the capability to infer biologically meaningful interactions. It is suitable for analyzing various binary-coded data and has the potential to facilitate further biological understanding with the discovery of additional coevolutionary networks.
Reconstructs a phylogenetic tree based on DNA or amino acid sequence data. IQPNNI combines various fast algorithms to generate a list of potential candidate trees. It was applied to two large data sets, the small subunit rRNA alignment (218 species, 4,182 bp) and the rbcl-gene alignment (500 species, 1398 bp) recently analyzed, and the results to PHYML and MetaPIGA were compared. The tool gives a slightly better accuracy than other programs tested. IQPNNI generates trees with similar high likelihoods.
A software tool for parameter-adaptive cophylogenetic analysis. Different from other event-based reconstruction methods CoRe-PA does not require any cost settings for the considered cophylogenetic events in advance, but seeks for the cheapest reconstruction in which the used costs are inversely related to the relative frequency of the corresponding event. The quality of the reconstructions obtained with CoRe-PA was analyzed experimentally on six coevolutionary systems. The results show that CoRe-PA is very useful when it is difficult or impossible to assign exact cost values to different types of coevolutionary events in advance.
A simple program for parsimony-based tree fitting. TreeFitter can handle arbitrary cost assignments fulfilling the requirements that duplication events, sorting events, and switches all have zero or positive cost associated with them. Codivergence events can be associated with either positive or negative cost (or zero cost).
Infers gene family evolution by speciation, gene duplication, horizontal gene transfer, and gene loss. RANGER-DTL consists of ten related programs designed to work together to support various reconciliation analyses. It enables the use of reconciliation-based gene tree and species tree reconstruction methods for prokaryotes. It permits analysis of gene families and offers several advanced features. It can also analyze trees with thousands of taxa.