PUG-2.1.1

Estimation of paralogs is now the default for PUG. If a paralog file is provided by the user, then it will be used.

Mapping information to nodes is now summarized and written to a new file.

Addition of an Rscript for making publication quality figures.

PUG-2.1.0

New features added:

--all_pairs option will give results for pairs from all species rather than just the unique LCAs. Allows user to identify copies retained in duplicate across whole clades.

--estimate_paralogs option will estimate putative in-paralogs within each gene tree based on the species available. This will create a file in the same format as the normal paralog file format. If this option is selected, you do not need to provide you own paralogs.

PUG-2.0.1

Adding the citability of PUG.

PUG-2.0

Major rewrites to streamline PUG from its use in various manuscripts. I now allow for a species tree to be used to building the tests to determine placement of the polyploid events. This replaces the confusing "hypothesis file" I used to use.

Since I have recently written this code, there may be some bugs. I am going to leave this in beta for a while until it has been tested more.