Phylogenetics
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Leaphy v.1.0 Beta
Likelihood estimation algorithms in phylogenetics. Leaphy uses maximum likelihood (ML) to estimate trees from aligned amino acid and nucleotide sequences under a variety of commonly used and popular models.The 1.
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NSG's voucher specimen database v.b.1.0.7
A database to handle voucher specimens of DNA sequences used for molecular phylogenetics.
Geneious Basic v.5.6.4
Geneious Basic is a software that speeds up and simplifies research in molecular biology and biochemistry. Geneious is a useful,
SplitsTree4 v.4.11.3
Phylogenetic networks computation made easy. SplitsTree4 is the leading software for computing unrooted phylogenetic networks from molecular sequence data. Given an alignment of sequences, a distance matrix or a set of trees,
FigTree v.1.3.1
FigTree is a graphical viewer of phylogenetic trees. It is a graphical viewer of phylogenetic trees and as a software for producing publication-ready figures. As with most of my programs, it was written for my own needs so may not be as polished and
STC (Shortest Triplet Clustering) v.1.2
Shortest Triplet Clustering. A new distance-based clustering method, triplet clustering algorithm (STC), to reconstruct phylogenies. The main idea is the introduction of a natural definition of so-called k-representative sets.
TreeStat v.1.2
Can process a set of trees in a PHYLIP or NEXUS format tree file. TreeStat is an software that can process a set of trees in a PHYLIP or NEXUS format tree file and calculate a number of summary statistics for each.
COAL v.1.0
COAL is a software for computing gene tree probabilities and simulating gene trees in species trees under the coalescent model. A tool for computing gene tree probabilities.
Seq-Gen v.1.3.2
Seq-Gen is a software that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process.
BaTS v.1.0 Beta Build 2
BaTS (Bayesian Tip-Significance testing), phylogeny-trait association is defined as the extent to which neighbouring taxa in a phylogenetic tree share a character of interest. This may be a classical phenotypic trait, a molecular attribute, disease
Murka v.1.3.1b
Murka (pronounced M-oo-rka, 'she-cat' in Russian) is a free program for inferring parsimonious phylogenies (i.e. trees of the minimal cost) from alignments of biological sequences.