Protocols

NCL specifications

Information


Unique identifier OMICS_20523
Name NCL
Alternative name Nexus Class Library
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.1.18
Stability Stable
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Paul Lewis
  • person_outline Mark Holder

Publication for Nexus Class Library

NCL citations

 (2)
call_split

Identification of the vascular plants of Churchill, Manitoba, using a DNA barcode library

2012
BMC Ecol
PMCID: 3538695
PMID: 23190419
DOI: 10.1186/1472-6785-12-25
call_split See protocol

[…] & ITS2). Analysis was performed using Maximum parsimony (MP) to establish if a particular taxon formed a monophyletic clade. Prior to analysis, fasta files were converted into Nexus format using the Nexus Class Library []. PAUP was then used to implement Parsimony analysis. Support for branching patterns was assessed using the parsimony ratchet []. Consensus tree was generated from a set of the m […]

library_books

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

2007
BMC Bioinformatics
PMCID: 1913543
PMID: 17559666
DOI: 10.1186/1471-2105-8-191

[…] sting software that uses NEXUS is mostly embedded in applications code such as PAUP* []. Some exceptions are the NEXUS methods provided by open-source toolkits such as BioPerl [], and by NCL [], for "NEXUS Class Library", a special purpose library written in C++. Most such implementations provide limited coverage of the NEXUS standard, and focus only on input and output of files, without providing […]

NCL institution(s)
Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
NCL funding source(s)
Supported by grant 98-4-5 ME from the Alfred P. Sloan Foundation/National Science Foundation.

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