.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.1.
.TH ALF "1" "September 2014" "alf 1.4.1+dfsg" "User Commands"
.SH NAME
alf \- Alignment free sequence comparison
.PP
SYNOPSIS
.IP
alf [OPTIONS] \fB\-i\fR IN.FASTA [\-o OUT.TXT]
.PP
DESCRIPTION
.IP
Compute pairwise similarity of sequences using alignment\-free methods in
IN.FASTA and write out tab\-delimited matrix with pairwise scores to
OUT.TXT.
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Displays this help message.
.HP
\fB\-\-version\fR
.IP
Display version information
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
When given, details about the progress are printed to the screen.
.IP
Input / Output:
.HP
\fB\-i\fR, \fB\-\-input\-file\fR FILE
.IP
Name of the multi\-FASTA input file. Valid filetypes are: fa and
fasta.
.HP
\fB\-o\fR, \fB\-\-output\-file\fR FILE
.IP
Name of the file to which the tab\-delimtied matrix with pairwise
scores will be written to. Default is to write to stdout. Valid
filetype is: alf.tsv.
.IP
General Algorithm Parameters:
.HP
\fB\-m\fR, \fB\-\-method\fR METHOD
.IP
Select method to use. One of N2, D2, D2Star, and D2z. Default: N2.
.HP
\fB\-k\fR, \fB\-\-k\-mer\-size\fR K
.IP
Size of the k\-mers. Default: 4.
.HP
\fB\-mo\fR, \fB\-\-bg\-model\-order\fR ORDER
.IP
Order of background Markov Model. Default: 1.
.IP
N2 Algorithm Parameters:
.HP
\fB\-rc\fR, \fB\-\-reverse\-complement\fR MODE
.IP
Which strand to score. Use both_strands to score both strands
simultaneously. One of input, both_strands, mean, min, and max.
Default: input.
.HP
\fB\-mm\fR, \fB\-\-mismatches\fR MISMATCHES
.IP
Number of mismatches, one of 0 and 1. When 1 is used, N2 uses the
k\-mer\-neighbour with one mismatch. Default: 0.
.HP
\fB\-mmw\fR, \fB\-\-mismatch\-weight\fR WEIGHT
.IP
Real\-valued weight of counts for words with mismatches. Default:
0.1.
.HP
\fB\-kwf\fR, \fB\-\-k\-mer\-weights\-file\fR FILE.TXT
.IP
Print k\-mer weights for every sequence to this file if given. Valid
filetype is: txt.
.PP
CONTACT AND REFERENCES
.IP
For questions or comments, contact:
.IP
Jonathan Goeke <goeke@molgen.mpg.de>
.IP
Please reference the following publication if you used ALF or the N2 method for your analysis:
.IP
Jonathan Goeke, Marcel H. Schulz, Julia Lasserre, and Martin
Vingron. Estimation of Pairwise Sequence Similarity of Mammalian
Enhancers with Word Neighbourhood Counts. Bioinformatics (2012).
.IP
Project Homepage:
.IP
http://www.seqan.de/projects/alf
.PP
VERSION
.IP
alf version: 1.1
Last update January 5, 2012