Cipres Science Gateway | POY Information

POY

POY4 is a flexible, multi-platform program for phylogenetic analysis of molecular and other data. An essential feature of POY4 is that it implements the concept of dynamic homology [27, 28] allowing optimization of unaligned sequences. POY4 offers flexibility for designing heuristic search strategies and implements an array of algorithms including multiple random addition sequence, swapping, tree fusing, tree drifting, and ratcheting. As output, POY4 generates a comprehensive character diagnosis, graphical representations of cladograms and their user-specified consensus, support values, and implied alignments. POY4 provides a unified approach to co-optimizing different types of data, such as morphological and molecular sequence data. In addition, POY4 can analyze entire chromosomes and genomes, taking into account large-scale genomic events (translocations, inversions, and duplications).

The portal version of POY4 (currently V.4.1.1) has limited functionality in terms of the number and kind of the input files permitted, as well as the classes of evolutionary events that are taken into account.

The POY manual is available at the POY home page here.

INPUT= up to 5 files in any of the following formats:
1. For unaligned sequences (The portal supports nucleotide sequences, allowing insertions, deletions, and substitutions events only):
         a. FASTA file format. Each file must contain one homologous fragment for all the species where it is present.
         b. NEXUS format with unaligned blocks (a single file may contain multiple unaligned blocks).
2. Prealigned sequences/Morphological Matrices:
         a. hennig/nona/TNT
   b. NEXUS

Test input file (nucleic acid): POY_in.txt

Test output file1 (analyzed data summary): POY_out_result.txt

Test output file2 (implied alignments of the most parsimonious trees, for all loaded sequences): POY_out_align.txt

Test output file3 (besttree): POY_trees.dnd.txt

If you use POY, please cite:

Varón, A., L. S. Vinh, W. C.Wheeler. 2010. POY version 4: phylogenetic analysis using dynamic homologies. Cladistics. 26: in press. http://research.amnh.org/scicomp/projects/poy.php.

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