Suggested Readings
Workshop on Molecular Evolution
Fundamentals of Molecular Evolution (Graur and Li 2000)
Molecular Evolution (Li 1997)
Molecular Evolutionary Genetics (Nei 1987)
The phylogenetic inference chapter in Molecular Systematics (Swofford et al. 1996)
Molecular Evolution: A Phylogenetic Approach (Page and Holmes 1998)
Two review papers, authored by Paul Lewis and Mark Holder (Lewis 2001, Holder and Lewis 2003)
Workshop on Genomics
Modern Genome Sequencing Technology
A decade’s perspective on DNA sequencing technology
Next-generation DNA sequencing methods
The impact of next-generation sequencing technology on genetics
Field guide to next-generation DNA sequencers
Bioinformatics for High Throughput Sequencing
Genome Structure Variation
Genome structural variation discovery and genotyping
Mapping copy number variation by population-scale genome sequencing
Transcriptomics
Computational methods for transcriptome annotation and quantification using RNA-seq
Computation for ChIP-seq and RNA-seq studies
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Genome-wide mapping of in vivo protein-DNA interactions
Assembly
De novo transcriptome assembly with ABySS
Velvet: algorithms for de novo short read assembly using de Bruijn graphs
Aligning short sequencing reads with Bowtie.
Galaxy
Integrating diverse databases into an unified analysis framework: a Galaxy approach
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.
GMOD/Gbrowse
The generic genome browser: a building block for a model organism system database
Getting Started with GMOD
Metagenomics
A Primer on Metagenomics
QIIME allows analysis of high-throughput community sequencing data
Supervised classification of human microbiota
Programming
Getting Started with BioPerl
PyCogent: a toolkit for making sense from sequence
