Bioconductor

Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language,

• 3.2. Practice
• 1.2. Prerequisites

CRAN

The

FASTA

A widely used sequence format, which has a sequence label beginning with '>', followed by the sequence.

• 2.2.1. Retrieving sequences example
• 2.1. Theory
• 9.2.1. MrBayes example
• 4.2.1. Neighbour joining example
• 1.1. Practice
• 6.2.3. Tree reconstruction exercise
• 6.2.1. Model choice example
• 6.2.2. RAxML example
• 5.2. Practice
• 11.2.1. 'Mugration' exercise

GI

A GI (genInfo) number is a sequence identifier used by GenBank. More information can be found here.

• 2.2. Practice
• 2.1. Theory

R-Forge

TN93

The Tamura-Nei model of nucleotide substitution. See this Wikipedia entry for details of this and other models of DNA evolution.

• 4.2.1. Neighbour joining example
• 4.1. Theory
• 1.1. Practice
• 6.2.1. Model choice example
• 5.2. Practice
• 11.2.1. 'Mugration' exercise

phylogeny

A phylogeny is a branching diagram or tree showing the inferred evolutionary relationships among various biological species, based on differences in their physical or genetic characteristics Wikipedia entry.

• 3.1. Theory
• 1. Background
• 6.2. Practice
• 6.1. Theory
• 10. Effective population size estimation
• 5.2. Practice
• 8.2. Practice
• 8.1. Theory