.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH TRF "1" "June 2020" "trf 4.09.1" "User Commands"
.SH NAME
trf \- locate and display tandem repeats in DNA sequences
.SH SYNOPSIS
.B trf
(File|Match|Mismatch|Delta|PM|PI|Minscore|MaxPeriod) [options]
.SH OPTIONS
Where: (all weights, penalties, and scores are positive)
.TP
File
sequences input file
.TP
Match
matching weight
.TP
Mismatch
mismatching penalty
.TP
Delta
indel penalty
.TP
PM
match probability (whole number)
.TP
PI
indel probability (whole number)
.TP
Minscore
minimum alignment score to report
.TP
MaxPeriod
maximum period size to report
.SS [options] = one or more of the following:
.TP
\fB\-m\fR
masked sequence file
.TP
\fB\-f\fR
flanking sequence
.TP
\fB\-d\fR
data file
.TP
\fB\-h\fR
suppress html output
.TP
\fB\-r\fR
no redundancy elimination
.TP
\fB\-l\fR <n>
maximum TR length expected (in millions) (eg, \fB\-l\fR 3 or \fB\-l\fR=\fI\,3\/\fR for 3 million)
Human genome HG38 would need \fB\-l\fR 6
.TP
\fB\-ngs\fR
more compact .dat output on multisequence files, returns 0 on success.
Output is printed to the screen, not a file. You may pipe input in with
this option using \- for file name. Short 50 flanks are appended to .dat
output.
.SH SEE ALSO
See more information on the TRF Unix Help web page: https://tandem.bu.edu/trf/trf.unix.help.html
.SH NOTE
Note the sequence file should be in FASTA format:
.PP
>Name of sequence
aggaaacctgccatggcctcctggtgagctgtcctcatccactgctcgctgcctctccag
atactctgacccatggatcccctgggtgcagccaagccacaatggccatggcgccgctgt
actcccacccgccccaccctcctgatcctgctatggacatggcctttccacatccctgtg
.SH AUTHOR
Copyright \(co 1999\-2020 Gary Benson
.P
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.