Phylogenetic Likelihood Library:
A highly optimized and parallized library for rapid prototyping and development of
likelihood based phylogenetic inference codes.
A pipeline that automatically updates reference trees using RAxML-Light when new sequences for the clade of interest appear
on GenBank or are added by the user.
A strapped down checkpointable RAxML version for computing huge trees on supercomputers.
Development of this code has stopped, please use ExaML instead!
A simple graphical tree comparison tool that visualizes differences
between up to four different trees by highlighting the branches
(bipartitions/splits) that are not shared among those trees.
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 and checkpointable tool that implements a composite likelihood ratio test for detecting selective sweeps.
SweeD is based on the SweepFinder algorithm.
A parallel tool for rapid & scalable detection of selective sweeps in whole-genome datasets using the omega statistic.
Web services
RAxML-Light Web-Service
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
here.
Small program to compute the number of possible rooted and unrooted binary trees for n taxa or
to compute the number of possible binary trees given a multi-furcating constraint tree.
A database comprising more than 60,000 inferred trees
and respective model parameter estimates from fully anonymized empirical datasets that were
analyzed using RAxML and RAxML-NG on the web servers at the
San Diego Supercomputer Center and the
SIB Swiss Institute of Bioinformatics.
A tool to predict the difficulty of phylogenetic analysis of Multiple Sequence Alignments (MSA).
Predicting the difficulty using Pythia is substantially faster than inferring multiple ML trees using RAxML-NG.
Pythia can be used to increase user awareness with respect to the amount of signal and uncertainty to be expected in phylogenetic analyzes,
and hence inform an appropriate (post-)analysis setup.