Literature DB >> 16267087

Nexplorer: phylogeny-based exploration of sequence family data.

Vivek Gopalan1, Wei-Gang Qiu, Michael Z Chen, Arlin Stoltzfus.   

Abstract

SUMMARY: Nexplorer is a web-based program for interactive browsing and manipulation of character data in NEXUS format, well suited for use with alignments and trees representing families of homologous genes or proteins. Users may upload a sequence family dataset, or choose from one of several thousand already available. Nexplorer provides a flexible means to develop customized views that combine a tree and a data matrix or alignment, to create subsets of data, and to output data files or publication-quality graphics. AVAILABILITY: Web access is from http://www.molevol.org/nexplorer

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Year:  2005        PMID： 16267087      PMCID： PMC1615790          DOI： 10.1093/bioinformatics/bti747

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


  3 in total

1.  NEXUS: an extensible file format for systematic information.

Authors:  D R Maddison; D L Swofford; W P Maddison
Journal:  Syst Biol       Date:  1997-12       Impact factor: 15.683

2.  Pandit: a database of protein and associated nucleotide domains with inferred trees.

Authors:  Simon Whelan; Paul I W de Bakker; Nick Goldman
Journal:  Bioinformatics       Date:  2003-08-12       Impact factor: 6.937

3.  Conservation versus parallel gains in intron evolution.

Authors:  Alexander V Sverdlov; Igor B Rogozin; Vladimir N Babenko; Eugene V Koonin
Journal:  Nucleic Acids Res       Date:  2005-03-23       Impact factor: 16.971
  3 in total
  5 in total

1.  Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data.

Authors:  Thomas Hladish; Vivek Gopalan; Chengzhi Liang; Weigang Qiu; Peter Yang; Arlin Stoltzfus
Journal:  BMC Bioinformatics       Date:  2007-06-08       Impact factor: 3.169

2.  CDAO-store: ontology-driven data integration for phylogenetic analysis.

Authors:  Brandon Chisham; Ben Wright; Trung Le; Tran Cao Son; Enrico Pontelli
Journal:  BMC Bioinformatics       Date:  2011-04-15       Impact factor: 3.307

3.  NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

Authors:  Rutger A Vos; James P Balhoff; Jason A Caravas; Mark T Holder; Hilmar Lapp; Wayne P Maddison; Peter E Midford; Anurag Priyam; Jeet Sukumaran; Xuhua Xia; Arlin Stoltzfus
Journal:  Syst Biol       Date:  2012-02-22       Impact factor: 15.683

4.  Strategies for reliable exploitation of evolutionary concepts in high throughput biology.

Authors:  Anthony Levasseur; Pierre Pontarotti; Olivier Poch; Julie D Thompson
Journal:  Evol Bioinform Online       Date:  2008-05-08       Impact factor: 1.625

5.  BorreliaBase: a phylogeny-centered browser of Borrelia genomes.

Authors:  Lia Di; Pedro E Pagan; Daniel Packer; Che L Martin; Saymon Akther; Girish Ramrattan; Emmanuel F Mongodin; Claire M Fraser; Steven E Schutzer; Benjamin J Luft; Sherwood R Casjens; Wei-Gang Qiu
Journal:  BMC Bioinformatics       Date:  2014-07-03       Impact factor: 3.169
  5 in total

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