.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH ALIGNSETS.PY "1" "May 2020" "AlignSets.py 0.6.0" "User Commands"
.SH NAME
AlignSets.py \- Multiple aligns input sequences by group
.SH DESCRIPTION
usage: AlignSets.py [\-\-version] [\-h]  ...
.PP
Multiple aligns input sequences by group
.SS "help:"
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "subcommands:"
.IP
Alignment method
.TP
muscle
Align sequence sets using muscle.
.TP
offset
Align sequence sets using predefined 5' offset.
.TP
table
Create a 5' offset table by primer multiple alignment.
.SS "output files:"
.IP
align\-pass
.IP
multiple aligned reads.
.IP
align\-fail
.IP
raw reads failing multiple alignment.
.IP
offsets\-forward
.IP
5' offset table for input into offset subcommand.
.IP
offsets\-reverse
.IP
3' offset table for input into offset subcommand.
.SS "output annotation fields:"
.IP
None
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.