The pipeline here was developed as part of teaching NESCent
Phyloinformatics course, July 2007.

Jason Stajich
jason_stajich __AT__ berkeley-DOT-EDU

Directories:
 genomes - input genome annotations in genbank file format

Workflow:
1. get_cds.pl - extract coding and protein sequence from genbank files to
                'cds' and 'protein' directories
2. run_blast.pl - run WU-BLASTP on the proteins files to generate all-vs-all
                  pairwise
3. make_clusterortho_files.pl - make orthologous clusters by single-linkage
                   insuring single copy.
4. make_clusterfamily_files.pl - make paralogous families by single-linkage
5. make_cluster_files.pl - make sequence fasta files from cluster data.
                           run on either the ortholog or gene family cluster 
                           files (two columns, 1st is cluster ID, 
                           second is gene id)
6. make_alignments.pl - Run a MSA alignment tool on the cluster fasta files

7. make_cdsaln_from_pepaln.pl - make CDS alignments from protein guide 
                                alignments

8. make_njtree.pl - Make an NJ tree and PS image using built in BioPerl module
                    on an alignment file.