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NAST-IER(1) User Commands NAST-IER(1)

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 database in FASTA format (seqs to NAST-align)

Optional: (unless defaults are not set!)

reference database in NAST format (default: /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta)
reference database in FASTA format (default: /usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta)
number of top hits to use for profile-alignment (default: 10)
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@debian.org> but can be freely used for any other distribution.

June 2013 nast-ier