This section is very much under development, but will eventually be home to lots of resources for learning about bacterial genomics…including primers for people getting started in biology, bioinformatics or sequencing…as well as specific resources in bacterial genomics, phylogenetics, molecular evolution and related topics.
Primers in biology for computer scientists, bioinformatics for life scientists, and next gen sequencing for everybody
- See this post of mine about bacterial populations and bacterial communities, and some of my work in this area
- Population structure, species concepts, horizontal transfer, homologous recombination
- Microevolution, subtyping, phylogeography
- Bacterial communities and metagenomics
- Phylogeny for the faint of heart (Sandra Baldauf, 2003, Trends in Genetics)
- Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods (Aris-Brosou & Xia, 2008, Int J Plant Genomics)
- Phylogenetics course @ Berkeley
- Article on phylogenomics (Philippe et al, 2011, PLoS Biology). Includes an explanation of phylogenomics, and glossary of terms relating to phylogenetics & phylogenomics.
- 2011 Bodega workshop – Phylogenetics wiki. Lecture slides and tutorials from a workshop in March 2011. Covers software packages like MrBayes, RAxML, R, BEAST, BayesTraits and topics including model selection, divergence dating, discrete & continuous character evolution, diversification rates.
- PLoS Currents – Tree of Life
- Phyloseminar.Org – online seminars in phylogenetics!
Useful sources of information
- Databases: NCBI, EBI
- Forums: SEQanswers, BioStar
- Talks: SlideShare – Jon Eisen
- Bioinformatics (journal) – Next gen sequencing virtual issue
- Briefings in Bioinformatics (journal) – Second generation sequencing issue (Sep 2010)
- NCBI Bookshelfof online books, e.g.: