Computational phyloinformatics
From academy
Computational Phyloinformatics is an 10 to 14-day intensive summer workshop established at NESCent, but often co-sponsored and hosted at other institutions. The workshop aims to give biologists practical knowledge and hands-on programming skills in phyloinformatics. The curriculum changes form year to year, but has included PERL (BioPerl, BioPhyo), SQL (BioSQL, TreeBASE), JAVA (JEBL, PAL, Mesquite), R (Ape), HyPhy, and BioRuby.
Synopsis
Biologists are faced with ever-larger datasets, more complex evolutionary models, and increasingly elaborate analytical methods. Seldom is it sufficient to run a dataset with an off-the-shelf program on a desktop PC; increasingly, biologists need to write scripts to interface with internet services and databases, build analytical pipelines, customize analyses, and distribute computation over multiple processors. This course is designed for graduate students, postdocs, and researchers in phylogenetics interested in receiving practical, hands-on training in the use of scripting languages for solving phyloinformatics problems. Students will learn how to write basic phylogenetic or comparative analysis scripts, parse various data files, traverse and compute over trees, and make practical use of phylogenetic software libraries. These skills will be learned in a biological context, touching on a diverse array of topics such as analysis of large datasets, automation of supertree assembly, scripting multiple sequence alignment processing, gene duplication inference, querying for topological patterns in large collections of trees, etc. Participants leave the course with their laptops filled with working software and programming libraries to apply them to their own research projects.
