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

CoPAP
Web
Desktop

CoPAP Co-evolution of Presence-Absence Patterns

A package for accurate inference of coevolving characters as manifested by…

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…

COALA
Desktop

COALA COevolution Assessment by a Likelihood-free Approach

An automated method that, starting from two phylogenies representing sets of…

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…

CopyCat
Desktop

CopyCat COPhYlogenetiC Analysis Tool

Provides an easy and fast access to cophylogenetic analyses. CopyCat…

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…

ALE
Desktop

ALE Amalgamated likelihood estimation

Reconciles a sample of gene trees with a species tree. ALE is a probabilistic…

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…

CoRe-ILP
Desktop

CoRe-ILP

A tool for reconciling the phylogenetic trees of parasites with the trees of…

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…

TreeFitter
Desktop

TreeFitter

A simple program for parsimony-based tree fitting. TreeFitter can handle…

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…

EUCALYPT
Desktop

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…

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…

DTscore
Desktop

DTscore Duplication Tree score

Reconstructs tandem duplication tree. DTscore can use sophisticated sequence…

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…

Notung
Desktop

Notung

Offers a unified framework for incorporating duplication/loss parsimony into…

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…

CoRe-PA
Desktop

CoRe-PA

A software tool for parameter-adaptive cophylogenetic analysis. Different from…

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…

RANGER-DTL
Desktop

RANGER-DTL Rapid ANalysis of Gene family Evolution using Reconciliation-DTL

A software package for inferring gene family evolution by speciation, gene…

A software package for inferring gene family evolution by speciation, gene duplication, horizontal gene transfer, and gene loss. RANGER-DTL takes as input a gene tree (rooted or unrooted) and a…

Mowgli
Desktop

Mowgli

A fast and exact algorithm for reconciling a gene tree and a dated species…

A fast and exact algorithm for reconciling a gene tree and a dated species tree. Mowgli optimizes a parsimony criterion according to a model that incorporates all the above-mentioned events…

TreeMap
Desktop

TreeMap

A program for the analysis of how dependent phylogenies are related, by…

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…

Jane
Desktop

Jane

A software tool for the cophylogeny reconstruction problem. The input to Jane…

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…

IQPNNI
Desktop

IQPNNI

Reconstructs a phylogenetic tree based on DNA or amino acid sequence data.…

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…

forester
Desktop

forester

Infers gene duplication and speciation events on a gene tree. Forester is…

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,…

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