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…

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…

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…

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,…

TimeTree
Data

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…

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…

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…

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…

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