Software
ParGenes
A tool for massively parallel model selection and phylogenetic tree inference on thousands of genes using thousands of cores, based on …
Read moreSpeciesRax
A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss. It is available for …
Read moreNetRAX
A tool for accurate and fast maximum likelihood based inference of phylogenetic networks.It is available for download here.
Read moreGeneRax
A tool for species tree-aware maximum likelihood based gene family tree inference under gene duplication, transfer, and loss. Open-source code is …
Read moreExaML
Exascale Maximum Likelihood (ExaML): Code for extremely large-scale phylogenetic inference on supercomputers using MPI.
Read morePerpetyally updating trees
A pipeline that automatically updates reference trees using RAxML-Light when new sequences for the clade of interest appear on GenBank or …
Read moreParsimonator
A fast and simple open-source parsimony program for building phylogenies on DNA data.Hybrid MrBayes Parallelized Bayesian tree inference for large-scale …
Read moreRAxML next generation
The all new, from scratch re-design of RAxML: better, faster, more scalable, easier to use.
Read moreModelTest next generation
The all new faster ModelTest, superseding jModelTest and ProtTest.
Read moreRootDigger
RootDigger uses a non-reversible Markov model to compute the most likely root location on a given tree. It is available for …
Read moreLagrange-NG
Attention Biogeographers! We just released Lagrange-NG, a re-design of the popular Lagrange tool: it’s faster, runs in parallel, and has …
Read moreVisual Tree Comparer
A simple graphical tree comparison tool that visualizes differences between up to four different trees by highlighting the branches (bipartitions/splits) …
Read moreTree Visualization Tool (very old)
Old Tree visualization tool using treemaps and taxonomic information.
Read moreAxParafit
Highly optimized versions of Pierre Legendre’s Parafit and DistPCoA programs for statistical analysis of host-parasite coevolution.
Read moreDppdiv
An optimized (using vector intrinsics) and parallelized version (using OpenMP) of the DPPDIV (original code by Tracy Heath) code for estimating …
Read morePhylogenetic Binning tool
The code from the paper: S. Berger, R. Lücking, A. Stamatakis on “Morphology-based phylogenetic binning of the lichen genera Graphis …
Read moreForeSeqs
Prediction of missing sequences and branch lengths on phylogenies inferred using MSAs that have missing/gappy data.
Read moreMPTP
A substantially faster, more scalable, and more accurate version of our PTP tool for single locus species delimitation
Read moreSCRAPP
Species Counting on Reference trees viA Phylogenetic Placements – bridging the gap between phylogenetic placement results and alpha diversity metrics, with the …
Read morePythia
A tool to predict the difficulty of phylogenetic analysis of Multiple Sequence Alignments (MSA).It is available for download here.
Read morePEAR – 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 …
Read morelibgapmis
An ultrafast library for pairwise short-read alignment, based on GapMis, including accelerated SSE-based and GPU-based versions.
Read moregenesis
A toolkit for working with phylogenetic data, mainly for evolutionary placements of short NGS reads on a reference phylogenetic tree. The …
Read moreEvolutionary Placement Algorithm
Algorithm for placing short reads onto a given reference phylogeny. This is part of standard RAxML.
Read morePaPaRa
PArsimony-based Phylogeny-Aware Read alignment program. The tool uses a given multipe sequence alignment and corresponding reference tree to align short reads …
Read moreSATIVA
Semi-Automatic Taxonomy Improvement and Validation Algorithm. Identifies taxonomically mislabeled sequences and suggests corrections using EPA (Evolutionary Placement Algorithm).
Read moreEPA next generation
Stand-alone, much faster, and massively parallel re-implementation of the Evolutionary Placement Algorithm.
Read moreSoftWipe
A tool and benchmark for assessing adherence of scientific software to coding quality standards.It is available for download here.
Read moreMicrobenchmark 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 …
Read moreReconfigurable Architectures (FPGAs)
Reconfigurable architectures for Bioinformatics applications designed by our former lab member Dr. Nikos Alachiotis.
Read moreFile conversion scripts
Shell script for fasta to phylip conversion.Matlab programs by Lowie Li for fasta to phylip and&…
Read moreTreeCounter
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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