Software

.js-id-software

TransPhylo

Inference of Transmission Tree from a Dated Phylogeny

Treespace

Statistical Exploration of Landscapes of Phylogenetic Trees

Phylotop

An R package which provides tools for calculating and viewing topological properties of phylogenetic trees.

Transcluster

An R package for inferring and viewing transmission clusters from sequence alignments and sample dates.

Transnp

Tansmission inference using SNP data

Treenomial

An R package that provides functionality for creation and comparison of polynomials that uniquely describe trees.

Treetop

Compare tree shapes using integer labels: an R package.