Family Alignment Documentation
- 1 Introduction
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.
All of our examples are descriptions of bioinformatic workflows or pipelines. A workflow is comprised of a set of analytical applications, performing the analyses themselves, and some set of scripts that hand data to applications and take results from these same applications. One will also frequently encounter some set of critical filters (e.g. in English, "only write those sequences to a file that match the query sequence with a p < .0001" or "get all nucleotide sequences > 250 bp in length from the input file"), and these filtering steps may be performed by an application or by a script.
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/).
- Alignments and phylogenies for ~27,000 gene familes derived from 140 plant species