SeqVis: a tool for detecting compositional heterogeneity among aligned nucleotide sequences.
Compositional heterogeneity is a poorly appreciated attribute of aligned nucleotide and amino acid sequences. It is a common property of molecular phylogenetic data, and it has been found to occur across sequences and/or across sites. Most molecular phylogenetic methods assume that the sequences have evolved under globally stationary, reversible, and homogeneous conditions, implying that the sequences should be compositionally homogeneous. The presence of the above-mentioned compositional heterogeneity implies that the sequences must have evolved under more general conditions than is commonly assumed. Consequently, there is a need for reliable methods to detect under what conditions alignments of nucleotides or amino acids may have evolved. In this chapter, we describe one such program. SeqVis is designed to survey aligned nucleotide sequences. We discuss pros-et-cons of this program in the context of other methods to detect compositional heterogeneity and violated phylogenetic assumptions. The benefits provided by SeqVis are demonstrated in two studies of alignments of nucleotides, one of which contained 7542 nucleotides from 53 species.
Jermiin
Lars Sommer
LS
School of Biological Sciences, Centre for Mathematical Biology and Sydney Bioinformatics, University of Sydney, Sydney, Australia.
Ho
Joshua Wing Kei
JW
Lau
Kwok Wai
KW
Jayaswal
Vivek
V
D001483:Base Sequence / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry; D008969:Molecular Sequence Data; D012313:RNA / Q000737:chemistry; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software; D014584:User-Computer Interface
D012313:RNA; D004247:DNA