v1.1.alpha13: New guppy commands and fixes21 May 2012, by Erick
This will be the last release before we release the improved taxonomic classification code, which is still getting tuned.
There is some new guppy functionality that is useful for doing edge PCA and the like for big trees:
trim, which finds the subset of the tree that actually has reads placed on it, and the
--rep-edges flag for the splitify subcommands that just takes representatives of edge collections that are similar to one another.
rppr voronoi has also seen some new work, including a simple way of passing just a tree to voronoi (rather than a collection of placed reads) called
There is also an implementation of a variant of a classical heuristic, called Partitioning Among Medoids (PAM), to solve the ADCL problem, which will be explained in a manuscript to be submitted this month.
There is also the fairly self-explanatory
guppy unifrac and
guppy rarefy, and subcommand that turns jplace files in to CSV files called
As usual, see the CHANGELOG for more details.