Use Getopt::Long to handle cl options.
Initial commit. Keeps only families for which
fasta sequence information is actually present.
Initial commit of clades.pl script. Updated version of prune.pl
Initial commit. Essentially improved version of select_from_pruneout.pl
remove print statement
Default is muscle, and default is best alignment,
use -quick for much faster, lower quality alignment.
Move to using Getopt::Long
Add papaya. But this is obsolete, use clades.pl
Obsolete, use select_from_cladesout.pl
Move to Getopt::Long
Initial commit. Script to compare 2 cladesout files (e.g.
based on mafft and muscle alignments) and find consensus
membership in various categories.
Additional plots to show splits convergence. MB.pl comments.
Gives diagnostic message if can't open file.
Added some comments to describe use of script.
Avoids using each with array, for backwards compatibility.
Output all ids and their region, as well as summary
numbers.
output command line options
Now using Getopt::Long
Add Beet (Beta vulgaris) to negative species, and output
now has column for number of leaves in each clade found.
Default min (sum) bs support is now 0.