nast-ier − NAST-based DNA alignment tool
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.
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)
http://microbiomeutil.sourceforge.net/#A_NASTiEr
This manual page was written by Andreas Tille <tille AT debian DOT org> but can be freely used for any other distribution.