Phylogenetic tree-building methods use molecular data to represent the evolutionary history of genes and taxa. A recurrent problem is to reconcile the various phylogenies built from different genomic sequences into a single one. This task is generally conducted by a two-step…

Phylogenetic tree-building methods use molecular data to represent the evolutionary history of genes and taxa. A recurrent problem is to reconcile the various phylogenies built from different genomic sequences into a single one. This task is generally conducted by a two-step approach whereby a binary representation of the initial trees is first inferred and then a maximum parsimony (MP) analysis is performed on it. This binary representation uses a decomposition of all source trees that is usually based on clades, but that can also be based on triplets or quartets. Source text: Swenson et al., 2010.

A python framework which construct split-based supertrees with the computation…

A python framework which construct split-based supertrees with the computation of three majority-rule (MR)supertree variants and input trees (MR(-), MR(+) and MR(+)g). PluMiST searches tree space by…

Compiles and integrates multilocus sequence typing data from all five schemes…

Compiles and integrates multilocus sequence typing data from all five schemes for the B. cereus group often involved in food poisoning incidents. The isolates have been classified thank to the seven…

A software for the inference of an optimal species tree under duplication and…

A software for the inference of an optimal species tree under duplication and duplication-loss cost from a set of unrooted gene trees. Fasturec determines an optimal species tree from collections of…

Constructs supertrees and explore the underlying phylogenomic information from…

Constructs supertrees and explore the underlying phylogenomic information from partially overlapping datasets. Clann has been developed to provide implementations of several supertree methods. The…

A method based on a dynamic programming method developed to find an exact…

A method based on a dynamic programming method developed to find an exact solution to the Robinson-Foulds Supertree problem within a constrained search space. FastRFS has excellent accuracy in terms…

Approximates maximum likelihood supertree inference. L.U.St allows the…

Approximates maximum likelihood supertree inference. L.U.St allows the calculation of the approximate likelihood of a supertree, given a set of input trees, performs heuristic searches to look for…

Constructs a supernetwork from partial trees based on simulated annealing. SNSA…

Constructs a supernetwork from partial trees based on simulated annealing. SNSA generates a planar network, whereas Z-closure and Q-imputation potentially produce non-planar networks. This algorithm…

Provides a graphic user interface to construct supertrees using different…

Provides a graphic user interface to construct supertrees using different methods. Rainbow also provides tools to analyze the quality of the supertrees produced.

A methodology for generating simulated datasets suitable as inputs to supertree…

A methodology for generating simulated datasets suitable as inputs to supertree methods. The data generation process mirrors data collection processes used by systematists when gathering empirical…

A software tool for constructing supertrees from source phylogenies. SuperFine…

A software tool for constructing supertrees from source phylogenies. SuperFine is a meta-method that utilizes a novel two-step procedure in order to improve the accuracy and scalability of supertree…

Enables the user to quickly summarize consensual information of a set of trees…

Enables the user to quickly summarize consensual information of a set of trees and localize groups of taxa for which the data require consolidation. For k input trees spanning a set of n taxa, this…

Aims at inferring supertrees that satisfy the same appealing theoretical…

Aims at inferring supertrees that satisfy the same appealing theoretical properties as with PhySIC, while being as informative as possible under this constraint. The informativeness of a supertree is…

A triplet-based supertree approach to phylogenomics. SuperTriplets infers…

A triplet-based supertree approach to phylogenomics. SuperTriplets infers supertrees with branch support values. The method avoids several practical limitations of the triplet-based binary matrix…

A software tool for collecting, curating, storing and processing data ready for…

A software tool for collecting, curating, storing and processing data ready for inclusion in supertree analyses. STK does not build supertrees, however, it does include a number of functions to get…