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.
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.
Reconciles a sample of gene trees with a species tree. ALE is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. The ALE approach was implemented in the context of a reconciliation model, which allows for the duplication, transfer and loss of genes. ALE efficiently approximates the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
An automated method that, starting from two phylogenies representing sets of host and parasite species, allows extraction of information about the costs of the events in a most probable reconciliation. Given a pair of “known” host and parasite trees and a prior probability distribution associated with the events, COALA simulates the temporal evolution of a set of species (the parasites) following the evolution of another set (the hosts) as represented by the latter's known phylogenetic tree. In this way, it generates under different parameter values a number of simulated multilabeled parasite trees which are then compared with the known parasite tree.
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.
Provides an easy and fast access to cophylogenetic analyses. CopyCat incorporates a wrapper for the program ParaFit, which conducts a statistical test for the presence of congruence between host and parasite phylogenies. This tool offers various features, such as the creation of customized host-parasite association data and the computation of phylogenetic host/parasite trees based on the NCBI taxonomy.
Reconstructs tandem duplication tree. DTscore can use sophisticated sequence evolution models, such as those taking into account heterogeneous rates of evolution among sites, and obviates some fallbacks of the parsimony criterion: inconsistency, long branch attraction. It is suitable for heavy statistical reliability analysis of the reconstructed histories, with a time complexity in O(n4), where n is the number of observed repeated sequences.
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.
Performs statistical studies of host-parasite coevolution. AxParafit consists of an improvement of the Parafit approach. It can be applied for large-scale co-phylogenetic analyses, and allows computation and analyses of large cophylogenetic datasets. Moreover, this program has integrated into CopyCat tool.
Allows to determine reconciliation feasibility. PLCT aims to encode the set of species-specific loci that must be orthologous. It captures the constraints implied by the multiple loci and multiple samples. The tool complements existing bootstrap methods for measuring gene tree quality. It can definitively identify when a gene tree topology has been affected by reconstruction error or gene conversion.
A software tool for the cophylogeny reconstruction problem. The input to Jane is a file containing a "host" tree, a "parasite" tree, and a mapping of the tips of the parasite tree to tips of the host tree. The user may specify the costs of each of five types of events: cospeciation, duplication, duplication with host switch, loss, and failure to diverge. Jane then endeavors to find least cost mappings of the parasite tree onto the host tree subject to the given tip mapping.
A software tool that can find one optimal reconciliation of a pair of host and parasite trees, can compute the number of all optimal solutions, and can enumerate them all. The first two problems are handled in polynomial time, while the enumeration has a polynomial delay complexity. EUCALYPT also displays the classes of solutions observed, where two solutions are in a same class if the number of each event in the two is the same. EUCALYPT takes a nexus file as input and generates all the information related to the reconciliations.
A tool for reconciling the phylogenetic trees of parasites with the trees of their respective hosts. CoRe-ILP uses a simple event model, considering cospeciations and host switching events. Based on this model solutions with a maximal number of cospeciations (primary criterion), a minimal number of host switching events (secondary criterion), and a minimal number of interactions (tertiary criterion) is found. CoRe-ILP is feasible for cophylogenetic systems with multi-host parasites and polytomies and uses branch length information, provided with the trees, to filter possible solutions.
Considers duplications, transfers and losses of genes. MPR yields a fast and exact algorithm to infer time consistent and most parsimonious reconciliations. It optimizes a parsimony criterion according to a model that incorporates some events (speciation, duplication, loss and transfer). Simulations showed that the parsimony criterion performs satisfactorily under realistic conditions at the phylum level. The tool performs well even under realistic rates, transfers being in general less accurately recovered than duplications.
Serves for time-consistent reconciliation maps and characterizes for given event-labeled gene trees T and species trees S whether there exists a time-consistent reconciliation map. tc-recon is an algorithm that constructs a time-consistent reconciliation map if one exists. Moreover, this tool can be useful for researchers to address tree reconciliation problems.
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).
Conducts principal coordinate analysis (PCoA) by correcting for negative eigenvalues. DistPCoA can be employed to produce a Euclidean representation of a distance matrix. It computes a distance matrix from a raw data table. This tool can discover eigenvalues and eigenvectors of a square distance matrix. It can return eigenvalues during the principal coordinate analysis of semi-metric or non-metric distance measures.
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.
Infers gene duplication and speciation events on a gene tree. Forester is extremely simple, and its asymptotic worst case behavior is only realized on pathological data sets. We show empirically, using 1750 gene trees constructed from the Pfam protein family database, that it appears to be a practical (and often superior) algorithm for analyzing real gene trees.
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.