An optimized (using vector intrinsics) and parallelized version (using OpenMP)
of the DPPDIV (original code by Tracy Heath) code for estimating divergence times
with a dirichilet process prior.
Phylogenetic Binning tool
The code from the paper: S. Berger, R. Lücking, A. Stamatakis on
"Morphology-based phylogenetic binning of the lichen genera Graphis and Allographa (Ascomycota: Graphidaceae)
using molecular site weight calibration" is available for download here.
PArsimony-based Phylogeny-Aware Read alignment program. The tool uses a given multipe
sequence alignment and corresponding reference tree to align short reads for analysis with the
EPA (Evolutionary Placement Algorithm).
A parallel tool for rapid & scalable detection of selective sweeps in whole-genome datasets using the omega statistic.
Avaliable at the San Diego Supercomputer Center (supported by the NSF iPlant collaborative)
To use this service you will first need to create an iPlant login here
and subsequently log in on the CIPRES portal using your iPlant credentials.
WEB-Servers for evolutionary placement of short reads