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POY version 4: phylogenetic analysis using dynamic homologies
Author(s) -
Varón Andrés,
Vinh Le Sy,
Wheeler Ward C.
Publication year - 2010
Publication title -
cladistics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.323
H-Index - 92
eISSN - 1096-0031
pISSN - 0748-3007
DOI - 10.1111/j.1096-0031.2009.00282.x
Subject(s) - phylogenetic tree , documentation , inference , sequence (biology) , flexibility (engineering) , biology , computer science , inversion (geology) , artificial intelligence , data mining , computational biology , mathematics , statistics , genetics , programming language , paleontology , structural basin , gene
We present POY version 4, an open source program for the phylogenetic analysis of morphological, prealigned sequence, unaligned sequence, and genomic data. POY allows phylogenetic inference when not only substitutions, but insertions, deletions, and rearrangement events are allowed (computed using the breakpoint or inversion distance). Compared with previous versions, POY 4 provides greater flexibility, a larger number of supported parameter sets, numerous execution time improvements, a vastly improved user interface, greater quality control, and extensive documentation. We introduce POY’s basic features, and present a simple example illustrating the performance improvements over previous versions of the application. © The Willi Hennig Society 2009.