A substantially faster, more scalable, and more accurate version of our PTP tool for single locus species delimitation

An ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.

A toolkit for working with phylogenetic data, mainly for evolutionary placements of short NGS reads on a reference phylogenetic tree. The …

Algorithm for placing short reads onto a given reference phylogeny. This is part of standard RAxML.

PArsimony-based Phylogeny-Aware Read alignment program. The tool uses a given multipe sequence alignment and corresponding reference tree to align short reads …

A tool for analyzing and editing/correcting chromatogram data.

Semi-Automatic Taxonomy Improvement and Validation Algorithm. Identifies taxonomically mislabeled sequences and suggests corrections using EPA (Evolutionary Placement Algorithm).

Stand-alone, much faster, and massively parallel re-implementation of the Evolutionary Placement Algorithm.

A very fast forward-in-time simulator for population genetics.

A parallel and checkpointable tool that implements a composite likelihood ratio test for detecting selective sweeps. SweeD is based on the …