The Exelixis Lab


Enabling Research in Evolutionary Biology

Phylogenetic Inference

RAxML

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. L├╝cking, 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.

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.