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Exploring the Behavior of POY, a Program for Direct Optimization of Molecular Data
Author(s) -
Giribet Gonzalo
Publication year - 2001
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.1096-0031.2001.tb00105.x
Subject(s) - congruence (geometry) , computation , homology (biology) , partition (number theory) , fragment (logic) , mathematics , computer science , algorithm , theoretical computer science , combinatorics , biology , geometry , biochemistry , gene
The performance of the computer program for phyloge netic analysis, POY, and its two implemented methods, “optimization alignment” and “fixed‐states optimization,” are explored for four data sets. Four gap costs are analyzed for every partition; some of the partitions (the 18S rRNA) are treated as a single fragment or in increasing fragments of 3, 10, and 30. Comparisons within and among methods are undertaken according to gap cost, number of fragments in which the sequences are divided, tree length, character congruence, topological congruence, primary homology statements, and computation time.