Phylogenetic Pipeline

Table of Contents:

• Overview of analytical steps
• Software requirements
  • Genotyping
  • Multiple Sequence Alignment
  • Phylogenetic Inference
  • Testing the pipeline
• Configuring the phylogenetic pipeline
• Pipeline usage
  • Samples
  • Regions of interest
  • Genotyping
  • Multiple sequence alignment
  • Phylogenetic inference
  • Executing the pipeline
• Makefile description
• File structure

Warning

This section of the documentation is currently undergoing a complete rewrite, and may therefore be incomplete in places.

The Phylogenetic Pipeline is a pipeline designed for processing of (one or more) BAMs, in order to carry out genotyping of a set of regions of interest. Following genotyping, multiple sequence alignment may optionally be carried out (this is required if indels were called), and phylogenetic inference may be done on the regions of interest, using a supermatrix approach through ExaML.

Regions of interest, as defined for the Phylogenetic pipeline, are simply any set of regions in a reference sequence, and may span anything from a few short genomic regions, to the complete exome of complex organisms (tens of thousands of genes), and even entire genomes.

While the Phylogenetic pipeline is designed for ease of use in conjunction with the BAM pipeline, but can be used on arbitrary BAM files, provided that these follow the expected naming scheme (see the Pipeline usage section).