CME Group
Computational Molecular Evolution

Software

Software Phylogenetic Inference

RAxML

Our standard tool for Maximum-likelihood based phylogenetic inference.

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ExaML

Exascale Maximum Likelihood (ExaML): Code for extremely large-scale phylogenetic inference on supercomputers using MPI.

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Phylogenetic Likelihood Library

Phylogenetic Likelihood Library: A highly optimized and parallized library for rapid prototyping and development of likelihood based phylogenetic inference codes.

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Perpetyally updating trees

A pipeline that automatically updates reference trees using RAxML-Light when new sequences for the clade of interest appear on GenBank or …

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RAxML-Light

A strapped down checkpointable RAxML version for computing huge trees on supercomputers. Development of this code has stopped, please use …

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Parsimonator

A fast and simple open-source parsimony program for building phylogenies on DNA data.Hybrid MrBayes Parallelized Bayesian tree inference for large-scale …

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ExaBayes

Parallelized Bayesian tree inference for large-scale datasets.

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llpll

New, flexible low level phylogenetic likelihood library.

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RAxML next generation

The all new, from scratch re-design of RAxML: better, faster, more scalable, easier to use.

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ModelTest next generation

The all new faster ModelTest, superseding jModelTest and ProtTest.

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libpll-2

Second version of libpll, including site repeats optimization.

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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) …

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Tree Visualization Tool (very old)

Old Tree visualization tool using treemaps and taxonomic information.

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AxParafit

Highly optimized versions of Pierre Legendre’s Parafit and DistPCoA programs for statistical analysis of host-parasite coevolution.

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Rogue Taxon Identification

A new, scalable algorithm for rogue taxon identification.

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Dppdiv

An optimized (using vector intrinsics) and parallelized version (using OpenMP) of the DPPDIV (original code by Tracy Heath) code for estimating …

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Phylogenetic Binning tool

The code from the paper: S. Berger, R. Lücking, A. Stamatakis on “Morphology-based phylogenetic binning of the lichen genera Graphis …

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ForeSeqs

Prediction of missing sequences and branch lengths on phylogenies inferred using MSAs that have missing/gappy data.

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PTP

A tool for delimiting species on phylogenies and evolutionary placements.

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MPTP

A substantially faster, more scalable, and more accurate version of our PTP tool for single locus species delimitation

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Next Generation Sequencing & Sequence Analysis

PEAR – Paired-End reAd mergeR

An ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just …

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GapMis

A tool for flexible pairwise sequence alignment with a variable, but bounded, number of gaps.

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libgapmis

An ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.

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genesis

A toolkit for working with phylogenetic data, mainly for evolutionary placements of short NGS reads on a reference phylogenetic tree. The …

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Evolutionary Placement Algorithm

Algorithm for placing short reads onto a given reference phylogeny. This is part of standard RAxML.

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PaPaRa

PArsimony-based Phylogeny-Aware Read alignment program. The tool uses a given multipe sequence alignment and corresponding reference tree to align short reads …

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MoTeX

An accurate and efficient tool for MoTif eXtraction.

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ChromatoGate

A tool for analyzing and editing/correcting chromatogram data.

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SATIVA

Semi-Automatic Taxonomy Improvement and Validation Algorithm. Identifies taxonomically mislabeled sequences and suggests corrections using EPA (Evolutionary Placement Algorithm).

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EPA next generation

Stand-alone, much faster, and massively parallel re-implementation of the Evolutionary Placement Algorithm.

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Population Genetics

AnA-FiTS

A very fast forward-in-time simulator for population genetics.

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Sweed

A parallel and checkpointable tool that implements a composite likelihood ratio test for detecting selective sweeps. SweeD is based on the …

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OmegaPlus

A parallel tool for rapid & scalable detection of selective sweeps in whole-genome datasets using the omega statistic.

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Web Services

RAxML-Light Web-Service

Available at the San Diego Supercomputer Center (supported by the NSF iPlant collaborative) To use this service you will first need …

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WEB-Servers for evolutionary placement of short reads

Our basic serverFancy Swiss Server

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Rogue Taxon Identification Web-Server

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PTP Web-Service

Access the web server for species delimitation using our new PTP method.

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RAxML Web Servers

Vital IT unit of the Swiss Institute of BioinformaticsCIPRES portal at San Diego Supercomputer CenterNew beta-version of the CIPRES portal&…

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MPTP Web Server

Access the new species delimitation web service using the new mptp approach.

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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 …

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Reconfigurable Architectures (FPGAs)

Reconfigurable architectures for Bioinformatics applications designed by our former lab member Dr. Nikos Alachiotis.

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File conversion scripts

Shell script for fasta to phylip conversion.Matlab programs by Lowie Li for fasta to phylip and&…

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TreeCounter

Small program to compute the number of possible rooted and unrooted binary trees for n taxa or to compute the number …

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