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Cophylogeny reconstruction software tools | Phylogenomics data analysis

Cophylogeny is the reconstruction of ancient relationships among ecologically linked groups of organisms from their phylogenetic information. Source text: Baudet et al., 2015.

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RANGER-DTL / Rapid ANalysis of Gene family Evolution using Reconciliation-DTL
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.
CoPAP / Co-evolution of Presence-Absence Patterns
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.
ALE / Amalgamated likelihood estimation
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.
COALA / COevolution Assessment by a Likelihood-free Approach
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.
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.
EUCALYPT / EnUmerator of Co-evolutionary Associations in PoLYnomial-Time delay
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.
MPR / Most Parsimonious Reconciliation
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.
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.
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