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.
A fast, parallel, and accurate Illumina paired-end read merger.
There is the PEAR documentation
and a Google Group for PEAR users.
The old PEAR page is not longer maintained,
but still might contain some relevant information.
A toolkit for working with phylogenetic data, mainly for evolutionary placements of short
NGS reads on a reference phylogenetic tree. The library supports many data types for
phylogenetics, sequences, taxonomis, as well as a plethora of utility functions and tools.
See also genesis-lib.org.
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).
Analysis and visualization tool, mainly for metagenomic sequence analysis, which implements
our phylogenetic placement pre- and post-processing methods, such as Edge Correlation, Phylogentic k-means,
Placement-Factorization, and many others.
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 RAxML-NG
The brand new web-server for the completely re-designed version of RAxML, called RAxML-NG is available