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.
As of 2023 Alexis will establish a new research group called Biodiversity Computing Group (BCG) at the Institute of Computer Science of the Foundation for Research and Technology Hellas in Heraklion, Crete, Greece.
The new group is funded through an EU ERA chair project for a duration of five years and will closely collaborate with his existing research group in Heidelberg.
We will soon start hiring, there are 4 PhD and 2 PostDoc positions available. We will pay competitive salaries (80% of HITS salaries, i.e., difference of cost of living between Germany and Greece) including health and social insurance at all levels (PhD students, PostDocs, PI). We are looking for computer scientists, Bioinformaticians, and "programming Biologists" to fill these positions. If you are interested to work where other people go on vacations and wish to be notified once the application process opens please send an email to Alexis.
Check the Press Release
Applications for the 13th summer school on computational molecular evolution organized by Cilia Antoniou, Ziheng Yang, Adam Leache, and Alexandros Stamatakis from May 7-18 2023, in Crete, Greece are now open at the following link
Alexis was recently appointed as Affiliated Scientist at the Evolutionary Genetics and Paleogenomics (EGP) lab of the Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, in Heraklion, Crete, Greece. The lab mostly focuses on ancient DNA analysis and you can find the web-page here.
The connection to this research lab in Crete offers opportunities to conduct data analysis projects in the framework of Bachelor/Master theses for KIT students abroad.
Attention Biogeographers! We just released Lagrange-NG, a re-design of the popular Lagrange tool: it's faster, runs in parallel, and has better code quality:
It is available for download here
A tool and benchmark for assessing adherence of scientific software to coding quality standards.
It is available for download here.
A tool for accurate and fast maximum likelihood based inference of phylogenetic networks.
It is available for download here.
A tool for maximum likelihood species tree inference from gene family trees under duplication, transfer, and loss.
It is available for download here.
Species Counting on Reference trees viA Phylogenetic Placements - bridging the gap between phylogenetic placement results and alpha diversity metrics, with the possibility of further in-depth analysis.
It is available for download here
RootDigger uses a non-reversible Markov model to compute the most likely root location on a given tree.
It is available for download here
Our first tool for gene tree species tree reconciliation. Open-source code is available here, a respective preprint can be found here.
A tool for massively parallel model selection and phylogenetic tree inference on thousands of genes using thousands of cores, based on ModelTest-NG and RAxML-NG. Now published in Bionformatics and available for download here.
The brand new web-server for the completely re-designed version of RAxML, called RAxML-NG is available here.
The latest version of RAxML-NG, the complete re-design of RAxML can be found at Alexey's github repository.
RAxML questions, help & bug reports: please use the RAxML google group
The respective paper can be found here
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