Exelixis is the Greek word for evolution.
The background image is a view of Mount Psiloritis on the island of Crete in winter 2006.
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.
The scientific computing group, the home of RAxML, at the Heidelberg Institute for Theoretical Studies (HITS) in Heidelberg, Germany is soliciting applications for its visiting PhD student scholarship program.
Visits can last from 3 up to 6 months and we cover all travel expenses and also provide a scholarship of EUR 600 per month.
Applicants shall be enrolled in a Bioinformatics or computer science PhD program and work on likelihood-based phylogenetic inference.
The goal of the scholarship is to either extend or use the Phylogenetic Likelihood Library (PLL) we have recently released (see PLL). The PLL is a highly optimized and parallelized library that allows for computing the likelihood on phylogenetic trees.
Applicants shall send a short two page CV, a letter of recommendation by their PhD supervisor, and a one page abstract describing how they want to use/extend the PLL to Alexandros Stamatakis (Alexandros dot Stamatakis at h-its dot org) by January 31st 2014.
We will hold our 6th course on computational molecular evolution (with John Huelsenbeck, Bruce Rannalla, Olivier Gasucuel, Nich Goldman, Ziheng Yang, and colleagues) in Crete again in 2014 from May 5-14. For further info, please follow this link.
Tomas, Kassian, and Jiajie have developed a fast, parallel, and accurate Illumine paired-end read merger called PEAR. Please visit the PEAR page for further information.
We have made the phylogenetic likelihood library for rapid prototyping and development of phylogenetic analysis programs.
It is available under GNU GPL at libpll.
It has functions to calculate and optimize likelihoods and branch lengths, parse alignments and trees as well as to conduct tree search operations (NNIs, SPRs) on trees.
It is highly optimized and supports SSE3 as well as AVX vector intrinsics. It can run in parallel using PThreads on multi-core systems and MPI on massively parallel systems.
For instance, we have already used the library, to accelerate DPPDIV (a Bayesian program to calculate divergence times) by over a factor of 100. See this paper.
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