Enabling Research in Evolutionary Biology
Our focus is on the evolution of hardware and parallel computer architectures as well as on the evolution of molecular sequences.
We understand Bioinformatics as a discipline that develops algorithms, models, and tools that help Biologists to generate new biological insights and knowledge. We try to bridge the gap between the world of systematics and the world of high performance computing.
Due to the increasing descrepancy between the pace of molecular data accumulation and increase in CPU speeds (which is much slower), which we call the "Bio-Gap" we feel that the time has come to establish parallel computing as standard technique in Bioinformatics.
Applications are now open for the 10th summer school on computational molecular evolution organized by Nick Goldman, Ziheng Yang, Cilia Antoniou, Laura Emery and Alexis Stamatakis. It will be held once again in Heraklion, Crete, Greece.
See the course page for further details
The new, from scratch re-implementation of RAxML is finally avaible at github.
It's faster, more stable, easier to use, and more scalable
libpll is a new library that facilitates phylogenetic analyses. Libpll is a low-level re-design of our previous PLL, that offers unprecedented flexibility when implementing new models, testing hypotheses and/or developing new tools, methods or pipelines.
Apart from the highly-optimized phylogenetic likelihood function, libpll offers the following functionality:
Libpll is highly optimized and can make use of the SSE3/AVX/AVX-2 instruction sets. It is available for download here under the Affero GPL 3 License.
This tool is a significant improvement of our previous PTP tool for single-locus species delimitation. It is significantlky faster, more accurate, and more scalable with respect to the number of taxa.
The tool identifies taxonomically mislabeled sequences and suggests corrections using the EPA (Evolutionary Placement Algorithm).
For more details, please visit the SATIVA page. 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.
For more details, please visit the genesis page.
Tool for rrediction of missing sequences and branch lengths on phylogenies inferred using MSAs that have missing/gappy data.
For more details, please visit the ForeSeqs page.
We are always looking for student programmers (HiWis) and students interested in doing bachelor/master theses projects with us. If you are interested please send an email to Alexis at Alexandros dot Stamatakis at h hyphen its dot org