Dppdiv
An optimized (using vector intrinsics) and parallelized version (using OpenMP) of the DPPDIV (original code by Tracy Heath) code for estimating …
Phylogenetic Binning tool
The code from the paper: S. Berger, R. Lücking, A. Stamatakis on “Morphology-based phylogenetic binning of the lichen genera Graphis …
ForeSeqs
Prediction of missing sequences and branch lengths on phylogenies inferred using MSAs that have missing/gappy data.
MPTP
A substantially faster, more scalable, and more accurate version of our PTP tool for single locus species delimitation
libgapmis
An ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.
genesis
A toolkit for working with phylogenetic data, mainly for evolutionary placements of short NGS reads on a reference phylogenetic tree. The …
Evolutionary Placement Algorithm
Algorithm for placing short reads onto a given reference phylogeny. This is part of standard RAxML.
PaPaRa
PArsimony-based Phylogeny-Aware Read alignment program. The tool uses a given multipe sequence alignment and corresponding reference tree to align short reads …