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NAST-IER

NAME

nast-ier − NAST-based DNA alignment tool

DESCRIPTION

The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences.

The alignment algorithm involves global dynamic programming profile alignment to fixed (NAST-formatted) multiply aligned template sequences without any end-gap penalty.

NAST-iEr is part of the microbiomeutil suite.

OPTIONS

Required:
−−query_FASTA

query database in FASTA format (seqs to NAST−align)

Optional: (unless defaults are not set!)
−−db_NAST

reference database in NAST format (default: /usr/share/microbiomeutil−data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta)

−−db_FASTA

reference database in FASTA format (default: /usr/share/microbiomeutil−data/RESOURCES/rRNA16S.gold.fasta)

−−num_top_hits

number of top hits to use for profile−alignment (default: 10)

−−Evalue

Evalue cutoff for top hits (default: 1e−50)

SEE ALSO

http://microbiomeutil.sourceforge.net/#A_NASTiEr

AUTHOR

This manual page was written by Andreas Tille <tille AT debian DOT org> but can be freely used for any other distribution.

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