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)
AUTHOR
This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other distribution.