See  http://photobiontdiversity.wordpress.com/2013/05/15/green-algal-ph…onts-trebouxia
First Commit
Modified to handle metadata files with more than 4 columns
Added Trebouxia ITS reference accession
Added flexibility to handle metadata files with more than 4 columns
Added ability to colour by Trebouxia species
Simplified code and removed option to truncate sequences (this functionality is in trunc.pl)
Modified to exclude taxa listed as redundant rather than to include ones listed as IN TREE

This means that it includes uncategorized sequences
Modified to fetch 100 sequences at a time rather than all at once
Added option to parse Genbank files in addition to fasta headers

This option extracts the organism information as well as host information located in the
"host", "isoaltion_source" or "note" tags
Taxon names modified based on changes to Nostoc_rbcX_metadata.txt
Removed unneeded files