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@debian.org> but can be freely used
       for any other distribution.