POY is an open source, easy to use phylogenetic analysis application that supports multiple kinds of data (e.g. morphology, nucleotides, genes and gene regions, chromosomes, whole genomes, etc).
POY is particular in that it can perform true alignment and phylogeny inference (i.e. input sequences need not to be prealigned).
Insertions, deletions, and rearrangements, can then be included in the overall tree score (under Maximum Parsimony), or in the model (under Maximum Likelihood).
A variety of heuristic algorithms have been developed for this purpose and are implemented in POY.
Detailed instructions on how to install and use the POY utility on your Mac are available HERE.
What's New in This Release: [ read full changelog ]
· Consistency in alignment procedures across the application. The trace-back procedures produce the same result in affine (with gap opening equal to 0) as normal alignment procedures, as well as alignment procedures with speed increases (newkkonen), and the space saving algorithm.
· Continuous characters are fully supported above the range of 0-255, now 0 to the maximum size of integers on the machine. Although this change is slightly slower, characters that do fit in the 255 range are vectorized as previously implemented.
· build(N,random) does not do a random Wagner build, but generates and diagnoses a random topology.
· Sankoff and Sequence characters with matrices of non-0 diagonal elements have been implemented.
· Information theoretic model selection procedures have been designed under static and dynamic likelihood (see new command below). This command can be used on multiple character sets and types of data in which case the model selected for each data-set are combined on...