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Unclassified tools | Phylogenomics

STELLS2
Desktop

STELLS2

Computes the gene tree probability. STELLS2 is usually more accurate than…

Computes the gene tree probability. STELLS2 is usually more accurate than several existing methods when there is one allele per species. It outperforms these methods significantly when there are…

node dating
Desktop

node dating

Estimates the dates of the internal nodes of a phylogenetic tree. node.dating…

Estimates the dates of the internal nodes of a phylogenetic tree. node.dating is a divergence-time analysis software and uses a maximum-likelihood method. It can be extended to incorporate a variable…

ClonalOrigin
Desktop

ClonalOrigin

Allows to work about the history of recombination events that affected a given…

Allows to work about the history of recombination events that affected a given sample of bacterial genomes. ClonalOrigin run on as comparative analysis of sequences of a sample of bacterial genomes…

P4P
Web

P4P Peptidomes for Phylogenies

Enables the in silico inference of bacterial taxonomy through the analysis of…

Enables the in silico inference of bacterial taxonomy through the analysis of peptidomes. The P4P methodology uses whole genome data and in silico protein digestion to infer bacterial taxonomy,…

Phylesystem
Desktop

Phylesystem

Provides a git-based data store for archiving and curating phylogenetic…

Provides a git-based data store for archiving and curating phylogenetic estimates of species relationships. By incorporating curation into the data storage, Phylesystem have lowered the activation…

ClonalFrameML
Desktop

ClonalFrameML

Uses maximum likelihood inference to simultaneously detect recombination in…

Uses maximum likelihood inference to simultaneously detect recombination in bacterial genomes and account for it in phylogenetic reconstruction. ClonalFrameML can analyse hundreds of genomes in a…

SPIMAP
Desktop

SPIMAP Species Informed Maximum A Posteriori Gene Tree Reconstruction

Provides a phylogenetic reconstruction method specifically designed for…

Provides a phylogenetic reconstruction method specifically designed for reconstructing gene trees in the case of a known species tree. SPIMAP uses a Bayesian framework to model sequence evolution,…

SCOTTI
Desktop

SCOTTI Structured COalescent Transmission Tree Inference

Models each host as a distinct population, and transmissions between hosts as…

Models each host as a distinct population, and transmissions between hosts as migration events. This phylogenetic software can (i) infer transmission events, (ii) account for the uncertainty…

STRIDE
Desktop

STRIDE Species Tree Root Inference from gene Duplication Events

Identifies sets of well-supported gene duplication events from cohorts of gene…

Identifies sets of well-supported gene duplication events from cohorts of gene trees. STRIDE is an algorithm developed to analyze these duplication events to infer a probability distribution over an…

SPIDIR
Desktop

SPIDIR Species Informed Distance-based Reconstruction

Reconstructs gene-tree by using learning gene- and species-specific…

Reconstructs gene-tree by using learning gene- and species-specific substitution rates across multiple complete genomes. SPIDIR achieves significantly higher accuracy, addresses the species-level…

MAP-DP
Desktop

MAP-DP

Factorizes branch lengths into time and rates. MAP-DP is a Bayesian framework…

Factorizes branch lengths into time and rates. MAP-DP is a Bayesian framework easily adapted to take divergence time information into account, by restricting a speciation to a specific interval or…

tqDist
Desktop

tqDist

Computes the triplet and quartet distances between general rooted or unrooted…

Computes the triplet and quartet distances between general rooted or unrooted trees, respectively. The tqDist program is based on algorithms with running time O(n log n) for the triplet distance…

TimeTree
Dataset

TimeTree

Offers a public knowledge-base for information on the tree-of-life and its…

Offers a public knowledge-base for information on the tree-of-life and its evolutionary timescale. TimeTree is a web-based resource for researchers and educators from all fields of science to assist…

SaguaroGW
Desktop

SaguaroGW Saguaro Genome-Wide

Detects signatures of selection within populations, strains, or species.…

Detects signatures of selection within populations, strains, or species. Saguaro identifies regions under lineage-specific constraint for the first set, and genomic segments that we attribute to…

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