Literature DB >> 16766557

SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides.

Joshua W K Ho1, Cameron E Adams, Jie Bin Lew, Timothy J Matthews, Chiu Chin Ng, Arash Shahabi-Sirjani, Leng Hong Tan, Yu Zhao, Simon Easteal, Susan R Wilson, Lars S Jermiin.   

Abstract

UNLABELLED: 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. AVAILABILITY: http://www.bio.usyd.edu.au/jermiin/programs.htm.

Mesh：

Year:  2006        PMID： 16766557     DOI： 10.1093/bioinformatics/btl283

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  12 in total

1.  Species delimitation and phylogenetic relationships of Chinese Leishmania isolates reexamined using kinetoplast cytochrome oxidase II gene sequences.

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2.  Species discrimination and phylogenetic inference of 17 Chinese Leishmania isolates based on internal transcribed spacer 1 (ITS1) sequences.

Authors:  Bin-Bin Yang; Xian-Guang Guo; Xiao-Su Hu; Jian-Guo Zhang; Lin Liao; Da-Li Chen; Jian-Ping Chen
Journal:  Parasitol Res       Date:  2010-07-09       Impact factor: 2.289

3.  Reconstructing the evolutionary history of the radiation of the land snail genus Xerocrassa on Crete based on mitochondrial sequences and AFLP markers.

Authors:  Jan Sauer; Bernhard Hausdorf
Journal:  BMC Evol Biol       Date:  2010-10-04       Impact factor: 3.260

4.  Multiple origins of deep-sea Asellota (Crustacea: Isopoda) from shallow waters revealed by molecular data.

Authors:  Michael J Raupach; Christoph Mayer; Marina Malyutina; Johann-Wolfgang Wägele
Journal:  Proc Biol Sci       Date:  2009-03-07       Impact factor: 5.349

5.  Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood.

Authors:  Simon A Berger; Denis Krompass; Alexandros Stamatakis
Journal:  Syst Biol       Date:  2011-03-23       Impact factor: 15.683

6.  The complete mitochondrial genome of Flustra foliacea (Ectoprocta, Cheilostomata) - compositional bias affects phylogenetic analyses of lophotrochozoan relationships.

Authors:  Maximilian P Nesnidal; Martin Helmkampf; Iris Bruchhaus; Bernhard Hausdorf
Journal:  BMC Genomics       Date:  2011-11-23       Impact factor: 3.969

7.  Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics.

Authors:  Victor A Vera-Ruiz; Kwok W Lau; John Robinson; Lars S Jermiin
Journal:  BMC Bioinformatics       Date:  2014-01-31       Impact factor: 3.169

8.  Rampant nuclear insertion of mtDNA across diverse lineages within Orthoptera (Insecta).

Authors:  Hojun Song; Matthew J Moulton; Michael F Whiting
Journal:  PLoS One       Date:  2014-10-21       Impact factor: 3.240

9.  Molecular variation at a candidate gene implicated in the regulation of fire ant social behavior.

Authors:  Dietrich Gotzek; D Dewayne Shoemaker; Kenneth G Ross
Journal:  PLoS One       Date:  2007-11-07       Impact factor: 3.240

10.  Selecting optimal partitioning schemes for phylogenomic datasets.

Authors:  Robert Lanfear; Brett Calcott; David Kainer; Christoph Mayer; Alexandros Stamatakis
Journal:  BMC Evol Biol       Date:  2014-04-17       Impact factor: 3.260
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