Family Alignment Documentation
These pages describe approaches to characterizing sequence families in some set of related organisms. There are many ways to do this so our examples, though robust and proven by practice, are selected from a multitude of possible examples. The focus is on approaches that use a Bio* toolkit (BioJava, BioPerl, BioPython, BioRuby) since these packages offer the user different workflow possibilities but home-grown solutions are also discussed.
Analysis of Gene & Protein Families from Fungal Genomes
Based on the work of Jason Stajich (http://fungal.genome.duke.edu/).
Analysis of Silent Substitutions Within a Genome or Across Multiple Genomes
Based on the work of Amy Bouck (http://visionlab.bio.unc.edu/).
Reconciling the Multiple Trees Created by Analyzing Genomes
Based on the work of Stefanie Hartmann (http://visionlab.bio.unc.edu/).