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Start Your TrialPOY4 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 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 Gateway 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.
toolId=POY
Supported Parameters:
input.infile_ - Primary Input File
input.infile2_ - Input File
input.infile3_ - Input File
input.infile4_ - Input File
input.infile5_ - Input File
input.infile6_ - Input File
input.terminalsfile_ - Terminals file
input.synonymsfile_ - Synonyms file
input.constraint_ - Constraint file
vparam.runtime_ - Float - Maximum Hours to Run (up to 72 hours) (default=1.0)
vparam.substitutions_ - Integer -Substitution cost (default=1)
vparam.indels_ - Integer - Individual insertion and deletion cost (default=1)
vparam.gapopening_ - Integer - Gap opening cost (default=0)
vparam.outgroup_ - String - Outgroup .
vparam.randomseed_ - Integer - Random seed. (no default)
vparam.support_ - Excl - Support calculation (requires a tree in one of the input files) -jacknife;bremer; bootstrap. (no default)
vparam.pseudoreplicates_ = Integer - Number of pseudoreplicates for bootstrap and jakknife (no default)
vparam.remove_ = Integer - Percentage of characters to be removed per pseudoreplicate during jackknife (no default)