Literature DB >> 14630669

NCL: a C++ class library for interpreting data files in NEXUS format.

Paul O Lewis1.   

Abstract

UNLABELLED: The NEXUS Class Library (NCL) is a collection of C++ classes designed to simplify interpreting data files written in the NEXUS format used by many computer programs for phylogenetic analyses. The NEXUS format allows different programs to share the same data files, even though none of the programs can interpret all of the data stored therein. Because users are not required to reformat the data file for each program, use of the NEXUS format prevents cut-and-paste errors as well as the proliferation of copies of the original data file. The purpose of making the NCL available is to encourage the use of the NEXUS format by making it relatively easy for programmers to add the ability to interpret NEXUS files in newly developed software. AVAILABILITY: The NCL is freely available under the GNU General Public License from http://hydrodictyon.eeb.uconn.edu/ncl/ SUPPLEMENTARY INFORMATION: Documentation for the NCL (general information and source code documentation) is available in HTML format at http://hydrodictyon.eeb.uconn.edu/ncl/

Mesh:

Year:  2003        PMID: 14630669     DOI: 10.1093/bioinformatics/btg319

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


  8 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.  RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language.

Authors:  Sebastian Höhna; Michael J Landis; Tracy A Heath; Bastien Boussau; Nicolas Lartillot; Brian R Moore; John P Huelsenbeck; Fredrik Ronquist
Journal:  Syst Biol       Date:  2016-05-28       Impact factor: 15.683

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.  2matrix: A utility for indel coding and phylogenetic matrix concatenation(1.).

Authors:  Nelson R Salinas; Damon P Little
Journal:  Appl Plant Sci       Date:  2014-01-07       Impact factor: 1.936

5.  A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0.

Authors:  Adam L Bazinet; Derrick J Zwickl; Michael P Cummings
Journal:  Syst Biol       Date:  2014-04-30       Impact factor: 15.683

6.  Initial implementation of a comparative data analysis ontology.

Authors:  Francisco Prosdocimi; Brandon Chisham; Enrico Pontelli; Julie D Thompson; Arlin Stoltzfus
Journal:  Evol Bioinform Online       Date:  2009-07-03       Impact factor: 1.625

7.  Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

Authors:  Arlin Stoltzfus; Hilmar Lapp; Naim Matasci; Helena Deus; Brian Sidlauskas; Christian M Zmasek; Gaurav Vaidya; Enrico Pontelli; Karen Cranston; Rutger Vos; Campbell O Webb; Luke J Harmon; Megan Pirrung; Brian O'Meara; Matthew W Pennell; Siavash Mirarab; Michael S Rosenberg; James P Balhoff; Holly M Bik; Tracy A Heath; Peter E Midford; Joseph W Brown; Emily Jane McTavish; Jeet Sukumaran; Mark Westneat; Michael E Alfaro; Aaron Steele; Greg Jordan
Journal:  BMC Bioinformatics       Date:  2013-05-13       Impact factor: 3.169

8.  An Algorithm for Calculating the Probability of Classes of Data Patterns on a Genealogy.

Authors:  Jordan M Koch; Mark T Holder
Journal:  PLoS Curr       Date:  2012-12-14
  8 in total

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