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

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Hladish, Thomas ^a,b   Gopalan, Vivek ^a   Liang, Chengzhi ^a,c   Qiu, Weigang ^a,d   Yang, Peter ^a   Stoltzfus, Arlin ^a,e  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^d CITY UNIVERSITY OF NEW YORK   (United States)

^e NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL DATA; COMPARATIVE ANALYSIS; FORMAL FRAMEWORK; FORMAL GRAMMARS; NEW APPLICATIONS; OBJECT-ORIENTED INTERFACES; OBSERVED DATA; TERMINAL STATE;

APPLICATION PROGRAMS; BIOINFORMATICS; COMPUTER PROGRAMMING; FORESTRY; TREES (MATHEMATICS);

APPLICATION PROGRAMMING INTERFACES (API);

ARTICLE; BIOINFORMATICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA ANALYSIS; GENE LIBRARY; GENOME ANALYSIS; INFORMATION PROCESSING; PHYLOGENETIC TREE; PROTEIN ANALYSIS; BIOLOGY; CHROMOSOME MAP; COMPUTER LANGUAGE; GENETIC DATABASE; INFORMATION RETRIEVAL; METHODOLOGY; MOLECULAR EVOLUTION;

CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EVOLUTION, MOLECULAR; INFORMATION STORAGE AND RETRIEVAL; PROGRAMMING LANGUAGES; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 34447266447     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-191     Document Type: Article

References (21)

1. Harvey PH Pagel MD The Comparative Method in Evolutionary Biology Oxford Series in Ecology and Evolution Oxford, Oxford University Press 1991 285
2. Eisen JA Phylogenomics: Improving functional predictions for uncharacterized genes by evolutionary analysis Genome Res 1998 8 3 163-167 9521918
3. Gaucher EA Gu X Miyamoto MM Benner SA Predicting functional divergence in protein evolution by site-specific rate shifts Trends Biochem Sci 2002 27 6 315-321 10.1016/S0968-0004(02)02094-7 12069792
4. Maddison DR Swofford DL Maddison WP NEXUS: An extendible file format for systematic information Systematic Biology 1997 46 590-621 10.2307/ 2413497 11975335
5. Maddison W Maddison D Mesquite: A modular Programming System for Evolutionary Analysis http://spiders.arizona.edu/mesquite, University of Arizona NA 2000
6. Swofford DL PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sunderland, Mass., Sinauer Associates 4 1999 http://www.lms.si.edu/PAUP
7. Huelsenbeck JP Ronquist F MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 2001 17 8 754-755 10.1093/bioinformatics/17.8.754 11524383
8. Kosakovsky Pond SL Frost SD Muse SV HyPhy: Hypothesis testing using phylogenies Bioinformatics 2005 21 5 676-679 10.1093/bioinformatics/ bti079 15509596
9. Gu X Huang W Xu D Zhang H GeneContent: Software for whole-genome phylogenetic analysis Bioinformatics 2005 21 8 1713-1714 10.1093/ bioinformatics/bti208 15598840
10. Oakley TH Gu Z Abouheif E Patel NH Li WH Comparative methods for the analysis of gene-expression evolution: An example using yeast functional genomic data Mol Biol Evol 2005 22 40-50 10.1093/molbev/msh257 15356281
11. Stajich JE Block D Boulez K Brenner SE Chervitz SA Dagdigian C Fuellen G Gilbert JG Korf I Lapp H The Bioperl toolkit: Perl modules for the life sciences Genome Res 2002 12 1611-1618 187536 12368254 10.1101/gr.361602
12. Lewis PO NCL: A C++ class library for interpreting data files in NEXUS format Bioinformatics 2003 19 17 2330-2331 10.1093/bioinformatics/btg319 14630669
13. Zmasek CM Eddy SR ATV: Display and manipulation of annotated phylogenetic trees Bioinformatics 2001 17 4 383-384 10.1093/ bioinformatics/17.4.383 11301314
14. Felsenstein J PHYLIP (Phylogenetic inference package) Seattle, WA, Department of Genetics, University of Washington 3.57 1995
15. Gopalan V Qiu WG Chen MZ Stoltzfus A Nexplorer: Phylogeny-based exploration of sequence family data Bioinformatics 2006 22 1 120-121 1615790 16267087 10.1093/bioinformatics/bti747
16. Iglesias JR Gupta G Ranjan D Pontelli E Milligan B Logic Programming Technology for Interoperability between Bioinformatics Software Tools Springer-Verlag 2001 Lecture Notes in Computer Science #1990 153-168
17. Mangalam H The Bio* toolkits--a brief overview Brief Bioinform 2002 3 3 296-302 10.1093/bib/3.3.296 12230038
18. Vos R Bio::Phylo http://search.cpan.org/dist/Bio-Phylo/
19. Zmasek C Cannon E phyloXML • an XML language for phylogenies http://www.phyloxml.org
20. Comprehensive Perl Archive Network (CPAN) http://www.cpan.org
21. SourceForge http://sourceforge.net