Our standard tool for Maximum-likelihood based phylogenetic inference.
ExaML
Exascale Maximum Likelihood (ExaML): Code for extremely large-scale
phylogenetic inference on supercomputers using MPI.
Phylogenetic Likelihood Library
Phylogenetic Likelihood Library:
A highly optimized and parallized library for rapid prototyping and development of
likelihood based phylogenetic inference codes.
Perpetually updating trees
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.
RAxML-Light
A strapped down checkpointable RAxML version for computing huge trees on supercomputers.
Development of this code has stopped, please use ExaML instead!
Parsimonator
A fast and simple open-source parsimony program for building phylogenies on DNA data.
Hybrid MrBayes
A hybrid MPI/OpenMP version of MrBayes v3.1.2.
ExaBayes
Parallelized Bayesian tree inference for large-scale datasets.
Phylogenetic Post-Analysis
Visual Tree Comparer
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.
Tree Visualization Tool (very old)
Old Tree visualization tool using treemaps and taxonomic information.
AxParafit
Highly optimized versions of Pierre Legendre's Parafit and DistPCoA programs for
statistical analysis of host-parasite coevolution.
Rogue Taxon Identification
A new, scalable algorithm for rogue taxon identification.
Dppdiv
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.
Next Generation Sequencing & Sequence Analysis
PEAR
A fast, parallel, and accurate Illumina paired-end read merger.
GapsMis
A tool for flexible pairwise sequence alignment with a variable, but bounded, number of gaps.
libgapmis
An ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.
PTP
A tool for delimiting species on phylogenies and evolutionary placements.
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 for analysis with the
EPA (Evolutionary Placement Algorithm).
MoTeX
An accurate and efficient tool for MoTif eXtraction.
ChromatoGate
A tool for analyzing and editing/correcting chromatogram data.
SATIVA
Semi-Automatic Taxonomy Improvement and Validation Algorithm. Identifies taxonomically
mislabeled sequences and suggests corrections using EPA (Evolutionary Placement Algorithm).
Population genetics
AnA-FiTS
A very fast forward-in-time simulator for population genetics.
Sweed
A parallel and checkpointable tool that implements a composite likelihood ratio test for detecting selective sweeps.
SweeD is based on the SweepFinder algorithm.
OmegaPlus
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 evolutionary placement of short reads
Our basic server
Fancy Swiss Server
Rogue Taxon Identification Web-Server
access the server here.
PTP Web-Service
Access the web server for species delimitation using our new PTP method.
RAxML Web Servers
Vital
IT unit of the Swiss Institute of Bioinformatics
CIPRES
portal at San Diego Supercomputer Center
New beta-version of
the CIPRES portal that provides a full workbench
Miscellaneous
Microbenchmark for Denormalized Floating Point Numbers
A small benchmark code, mainly for teaching purposes that can be used to highlight the
performance impact of de-normalized floating point numbers.
Reconfigurable Architectures (FPGAs)
Reconfigurable architectures for Bioinformatics applications designed by our former lab member Dr. Nikos Alachiotis.
File conversion scripts
Shell script for fasta to phylip conversion.
Matlab programs by Lowie Li for fasta to phylip and
phylip to fasta conversion.
TreeCounter
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.