nast-ier - NAST-based DNA alignment tool

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

nast-ier                                            June 2013                                        NAST-IER(1)

       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.

       nast-ier - NAST-based DNA alignment tool

Required:--query_FASTA
              query database in FASTA format (seqs to NAST-align)

   Optional:(unlessdefaultsarenotset!)--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)

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