PyNAST: A flexible tool for aligning sequences to a template alignment

Bioinformatics

Volumn 26, Issue 2, 2010, Pages 266-267

  Caporaso, J Gregory ^a   Bittinger, Kyle ^b   Bushman, Frederic D ^b   Desantis, Todd Z ^c   Andersen, Gary L ^c   Knight, Rob ^a  

^a UNIVERSITY OF COLORADO   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 75249107844     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp636     Document Type: Article

References (7)

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2. DeSantis, T.Z. et al. (2006a) Greengenes, a chimera-checked 16s rRNA gene database and workbench compatible with ARB. Appl. Environ. Microbiol., 72, 5069-5072.
3. DeSantis, T.Z. et al. (2006b) NAST: a multiple sequence alignment server for comparative analysis of 16s rRNA genes. Nucleic Acids Res., 34, W394-W399.
4. Edgar, R.C. (2004) Muscle: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5, 113.
5. Katoh, K. et al. (2005) Mafft version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res., 33, 511-518.
6. Knight, R. et al. (2007) PyCogent: a toolkit for making sense from sequence. Genome Biol., 8, R171.
7. Thompson, J.D. et al. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.