POY version 4: phylogenetic analysis using dynamic homologies

Abstract

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 POYÕs basic features, and present a simple example illustrating the performance improvements over previous versions of the application.

Anatomically modern Carboniferous harvestmen demonstrate early cladogenesis and stasis in Opiliones

“…13, and analysed under direct optimization 28,29 with POY v. 4 (ref. 30) under three parameter sets, including equal weights and two sets with differential indel opening and extension costs (indel opening = 3, indel extension = 1), one with equal weights for all nucleotide transformations (3,221) and another with differential weights for transversions and transitions (3,211). A search strategy consisting of a timed search (2 h with TBR branch swapping and tree fusing) was used to save an initial set of trees, which were later used as input trees for an analysis with auto_sequence_partition 1 .…”

A New Crown-Group Frog (Amphibia: Anura) from the Early Cretaceous of Northeastern Inner Mongolia, China

“…Gene sequences were downloaded from Genbank (Benson et al, 2004) and aligned using the default settings in MUSCLE (Edgar, 2004). The analysis was performed under maximum parsimony criterion using POY 4.1.2 (Varon et al, 2010). All morphological characters were unordered and weighted equally.…”

Systematics of the Neotropical GenusLeptodactylusFitzinger, 1826 (Anura: Leptodactylidae): Phylogeny, the Relevance of Non-molecular Evidence, and Species Accounts

“…On the basis of the arguments of Padial et al (2014), we employed tree-alignment (e.g., Sankoff, 1975;Wheeler, 1996;Wheeler, 2012, 2013) in POY 4.1.3 (Varón et al, 2010), which tests hypotheses of nucleotide homology dynamically by optimizing unaligned DNA sequences directly onto alternative topologies (Kluge and Grant, 2006;Wheeler et al, 2006;Grant and Kluge, 2009) while simultaneously optimizing prealigned transformation series as standard static matrices.…”