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Reconciliation visualization software tools | Phylogenomics

Reconciliation methods aim at recovering the evolutionary processes that shaped the history of a given gene family including events such as duplications, transfers and losses by comparing the discrepancies between the topologies of the associated…
ecceTERA
Web
Desktop

ecceTERA

A program that implements a generic parsimony reconciliation algorithm, which…

A program that implements a generic parsimony reconciliation algorithm, which accounts for gene duplication, loss, and transfer (DTL) as well as speciation, involving sampled and unsampled lineages,…

SylvX
Desktop

SylvX

A reconciliation viewer which implements classical phylogenetic graphic…

A reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple…

DLCpar
Desktop

DLCpar

Infers a most parsimonious (MP) history of a gene family in the presence of…

Infers a most parsimonious (MP) history of a gene family in the presence of duplications, losses, and incomplete lineage sorting (ILS). DLCpar relies on a reconciliation structure, the labeled…

PentaPlot
Desktop

PentaPlot

Computes such dekapentagonal maps given an appropriate probability support…

Computes such dekapentagonal maps given an appropriate probability support matrix. PentaPlot utilizes a genetic algorithm with demes and a local search strategy to search for the optimal layout. The…

primetv
Desktop
Web

primetv

A reconciliation viewer. primetv is a simple and compact visualization program…

A reconciliation viewer. primetv is a simple and compact visualization program that is the first automatic tool for illustrating general tree reconciliations. It reads reconciled trees in an extended…

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…

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…

DTL-RnB
Web

DTL-RnB

A tool for browsing the potentially large landscape of maximum parsimony…

A tool for browsing the potentially large landscape of maximum parsimony reconciliations (MPRs) of pairs of phylogenetic trees (e.g., species and gene trees or host and parasite trees). DTL-RnB…

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