Reconciliation visualization software tools | Phylogenomics data analysis
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 gene and species trees. These methods are also used in the framework of host/parasite studies to recover co-diversification scenarios including co-speciation events, host-switches and extinctions.
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, within undated, fully dated or partially dated species trees. The ecceTERA reconciliation model and algorithm generalize or improve upon most published DTL parsimony algorithms for binary species trees and binary gene trees. Moreover, ecceTERA can estimate accurate species-tree aware gene trees using amalgamation.
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 coalescent tree (LCT), that simultaneously describes coalescent and duplication-loss history. It enables an exhaustive and efficient search over the space of reconciliations. The tool enable inferences of the complex evolution of gene families across a broad range of species and large data sets.
A reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking sub-reconciliations).
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 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 Newick format and outputs them as tree-within-tree illustrations in a range of graphic formats. Output attributes, such as colors and layout, can easily be adjusted by the user. To enhance the construction of input to primetv, two helper programs, readReconciliation and reconcile, accompany primetv.
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 software utilizes a genetic algorithm with demes and a local search strategy. The hybrid genetic algorithm performs satisfactorily even in those cases where the chosen genomes are so divergent that little phylogenetic information has survived in the individual gene families.
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 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 rompts the user for non-negative costs for duplication, transfer, and loss costs and a method for scoring event. The tool then displays a sequence of maximum parsimony reconciliations that, collectively, come close to maximizing the total sum of the scores of the events with respect to the given scoring function.
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