CME Group

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 are added by the user.

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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 ExaML instead!

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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 datasets.

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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) that are not shared among those trees.

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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 divergence times with a dirichilet process prior.

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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 and Allographa (Ascomycota: Graphidaceae) using molecular site weight calibration”.

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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 a few kilobytes of memory.

PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.

For technical questions and support please use the PEAR google group at:
https://groups.google.com/forum/#!forum/pear-users

PEAR Commercial

The PEAR creative commons license prohibits commercial use of the code. For testing and using PEAR on a commercial basis you need to purchase a commercial software license.

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PEAR Academic

If you are a member of an academic institution and you use this software solely for research purposes, you can download this. Academic use is defined as the deployment of PEAR for the sole purpose of analyzing scientific data with the clear objective to (i) make all data and analyses publicly as well as freely available (ii) intend to publish the results of these data analyses in peer-reviewed scientific journals. Integration into and redistribution of PEAR in larger software pipelines requires prior written approval by the owners. All other uses of PEAR are considered as non-academic.

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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 library supports data in jplace format and their visualization. It also offers some basic methods to work with trees and sequences.

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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 for analysis with the EPA (Evolutionary Placement Algorithm).

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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 SweepFinder algorithm.

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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 to create an iPlant login here and subsequently log in on the CIPRES portal using your iPlant credentials.

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WEB-Servers for evolutionary placement of short reads

Our basic server
Fancy 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 Bioinformatics
CIPRES portal at San Diego Supercomputer Center
New beta-version of the CIPRES portal that provides a full workbench

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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 numbers.

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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 phylip to fastaconversion.

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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 of possible binary trees given a multi-furcating constraint tree.

More Information

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