.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH TANTAN "1" "July 2015" "tantan 13" "User Commands"
.SH NAME
tantan \- low complexity and tandem repeat masker for biosequences
.SH SYNOPSIS
.B tantan
[\fI\,options\/\fR] \fI\,fasta-sequence-file(s)\/\fR
.SH DESCRIPTION
Find simple repeats in sequences
.SS "Options (default settings):"
.TP
\fB\-p\fR
interpret the sequences as proteins
.TP
\fB\-x\fR
letter to use for masking, instead of lowercase
.TP
\fB\-c\fR
preserve uppercase/lowercase in non\-masked regions
.TP
\fB\-m\fR
file for letter pair scores (+1/\-1, but \fB\-p\fR selects BLOSUM62)
.TP
\fB\-r\fR
probability of a repeat starting per position (0.005)
.TP
\fB\-e\fR
probability of a repeat ending per position (0.05)
.TP
\fB\-w\fR
maximum tandem repeat period to consider (100, but \fB\-p\fR selects 50)
.TP
\fB\-d\fR
probability decay per period (0.9)
.TP
\fB\-a\fR
gap existence cost (0)
.TP
\fB\-b\fR
gap extension cost (infinite: no gaps)
.TP
\fB\-s\fR
minimum repeat probability for masking (0.5)
.TP
\fB\-f\fR
output type: 0=masked sequence, 1=repeat probabilities,
.IP
2=repeat counts, 3=BED (0)
.TP
\fB\-h\fR, \fB\-\-help\fR
show help message, then exit
.TP
\fB\-\-version\fR
show version information, then exit
.SH "REPORTING BUGS"
Report bugs to: tantan@cbrc.jp
.br
Home page: http://www.cbrc.jp/tantan/