DESCRIPTION

Unfortunately this tools that comes in connection with wigeon(1) is not documented but it regards the options below. If you know better about its purpose please drop us a note using reportbug on your Debian system.

OPTIONS

Required:

--query_NAST

multi-fasta file containing query sequences in alignment format

--db_NAST

db in NAST format

--db_FASTA

db in fasta format (megablast formatted)

Common options

-n

number of top matching database sequences to compare to (default 15)

-R

min divergence ratio default: 1.007

-P

min percent identity among matching sequences (default 90)

Parameters to tune ChimeraMaligner:

Scoring parameters:

-M

match score (default: +5)

-N

mismatch penalty (default: -4)

-Q

min query coverage by matching database sequence (default: 70)

-T

maximum traverses of the multiple alignment (default: 1)

Flags:

--printAlignments

(default off)

-v

verbose

--exec_dir

cd here before running

AUTHOR

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