.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.9.
.TH MAF-CONVERT.PY "1" "May 2012" "maf-convert.py 199" "User Commands"
.SH NAME
maf-convert.py \- Convert MAF-format alignments to tabular format
.SH DESCRIPTION
.SS "Usage:"
.IP
maf\-convert.py \fB\-\-help\fR
maf\-convert.py axt my\-alignments.maf
maf\-convert.py blast my\-alignments.maf
maf\-convert.py html my\-alignments.maf
maf\-convert.py psl my\-alignments.maf
maf\-convert.py sam my\-alignments.maf
maf\-convert.py tab my\-alignments.maf
.PP
Read MAF\-format alignments & write them in another format.
.SH OPTIONS
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-p\fR, \fB\-\-protein\fR
assume protein alignments, for psl match counts
.TP
\fB\-d\fR, \fB\-\-dictionary\fR
include dictionary of sequence lengths in sam format
.TP
\fB\-l\fR LINESIZE, \fB\-\-linesize\fR=\fILINESIZE\fR
line length for blast and html formats (default: 60)