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SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides

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Date

2006

Authors

Ho, Joshua
Adams, Cameron L
Lew, Jie
Matthews, Timothy
Ng, Chiu
Shahabi-Sirjani, Arash
Tan, Leng
Zhao, Yu
Easteal, Simon
Wilson, Susan

Journal Title

Journal ISSN

Volume Title

Publisher

Oxford University Press

Abstract

Summary: Most phylogenetic methods assume that the sequences evolved under homogeneous, stationary and reversible conditions. Compositional heterogeneity in data intended for studies of phylogeny suggests that the data did not evolve under these conditions. SeqVis, a Java application for analysis of nucleotide content, reads sequence alignments in several formats and plots the nucleotide content in a tetrahedron. Once plotted, outliers can be identified, thus allowing for decisions on the applicability of the data for phylogenetic analysis.

Description

Keywords

Keywords: nucleotide derivative; article; cluster analysis; computer analysis; computer program; genetic heterogeneity; information processing; nonhuman; nucleotide sequence; phylogeny; priority journal; sequence alignment

Citation

URI

http://hdl.handle.net/1885/76761

Collections

ANU Research Publications

Source

Bioinformatics

Type

Journal article

Book Title

Entity type

Access Statement

License Rights

DOI

10.1093/bioinformatics/btl283

Restricted until

2037-12-31

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Description
01_Ho_SeqVis:_visualization_of_2006.pdf (94.5 KB)

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