PHYLOViZ 2.0: Providing scalable data integration and visualization for multiple phylogenetic inference methods

Bioinformatics

Volumn 33, Issue 1, 2017, Pages 128-129

  Nascimento, Marta ^a,b   Sousa, Adriano ^c   Ramirez, Mário ^d   Francisco, Alexandre P ^a,b   Carriço, João A ^d   Vaz, Cátia ^a,c  

^a INESC ID   (Portugal)

^b INSTITUTO SUPERIOR TÉCNICO   (Portugal)

^c INSTITUTO SUPERIOR DE ENGENHARIA DE LISBOA   (Portugal)

^d INSTITUTO DE MEDICINA MOLECULAR   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; BACTERIUM; BACTERIUM IDENTIFICATION; CLASSIFICATION; DNA SEQUENCE; GENETICS; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SOFTWARE;

BACTERIA; BACTERIAL TYPING TECHNIQUES; GENOME, BACTERIAL; MULTILOCUS SEQUENCE TYPING; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 85014853204     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw582     Document Type: Article

References (12)

1. Carriço,J.A. et al. (2013) Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution. Euro Surv., 18, 20382.
2. Feil,E.J. et al. (2004) eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data. J. Bacteriol., 186, 1518-1530.
3. Francisco,A.P. et al. (2009) Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. BMC Bioinformatics, 10, 152.
4. Francisco,A.P. et al. (2012) PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. BMC Bioinformatics, 13, 87.
5. Gronau,I. and Shlomo,M. (2007) Optimal implementations of UPGMA and other common clustering algorithms. Inf. Process. Lett., 104, 205-210.
6. Jolley,K.A. et al. (2001) Sequence type analysis and recombinational tests (START). Bioinformatics, 17, 1230-1231.
7. Maiden,M.C.J. et al. (2013) MLST revisited: the gene-by-gene approach to bacterial genomics. Nat. Rev. Microbiol., 11, 728-736.
8. Saitou,N. and Nei,M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
9. Sneath,P.H.A. and Sokal,R.R. (1973) Numerical Taxonomy: The Principles and Practice of Numerical Classification, 1st ed., WF Freeman and Co., San Francisco, 573.
10. Spratt,B.G. (1999) Multilocus sequence typing: molecular typing of bacterial pathogens in an era of rapid DNA sequencing and the internet. Curr. Opin. Microbiol., 2, 312-316.
11. Studier,J. and Keppler,K. (1988) A note on the neighbor-joining algorithm of Saitou and Nei. Mol. Biol. Evol., 5, 729-731.
12. Suderman,M. and Hallett,M. (2007) Tools for visually exploring biological networks. Bioinformatics, 23, 2651-2659.