.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.2.
.TH CM_TO_WIGEON "1" "June 2013" "cm_to_wigeon " "User Commands"
.SH NAME
cm_to_wigeon \- helper for wigeon (Pintail 16S DNA anomaly detection)
.SH DESCRIPTION
\fBUnfortunately 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.\fR
.SH OPTIONS
.SS Required:
.IP \fB\-\-query_NAST\fR
multi\-fasta file containing query sequences in alignment format
.IP \fB\-\-db_NAST\fR
db in NAST format
.IP \fB\-\-db_FASTA\fR
db in fasta format (megablast formatted)
.SS Common options
.IP \fB\-n\fR
number of top matching database sequences to compare to (default 15)
.IP \fB\-R\fR
min divergence ratio default: 1.007
.IP \fB\-P\fR
min percent identity among matching sequences (default 90)
.SS Parameters to tune ChimeraMaligner:
Scoring parameters:
.IP \fB\-M\fR
match score   (default: +5)
.IP \fB\-N\fR
mismatch penalty  (default: \fB\-4\fR)
.IP \fB\-Q\fR
min query coverage by matching database sequence (default: 70)
.IP \fB\-T\fR
maximum traverses of the multiple alignment  (default: 1)
.SS Flags:
.IP \fB\-\-printAlignments\fR
(default off)
.IP \fB\-v\fR
verbose
.IP \fB\-\-exec_dir\fR
cd here before running
.SH "SEE ALSO"
http://microbiomeutil.sourceforge.net/
.SH AUTHOR
This manual page was written by Andreas Tille <tille@debian.org> but can be freely used for any other
distribution.