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PROGRAM:
NAME
alf - Alignment free sequence comparison
SYNOPSIS
alf [OPTIONS] -i IN.FASTA [-o OUT.TXT]
DESCRIPTION
Compute pairwise similarity of sequences using alignment-free methods in IN.FASTA
and write out tab-delimited matrix with pairwise scores to OUT.TXT.
-h, --help
Displays this help message.
--version
Display version information
-v, --verbose
When given, details about the progress are printed to the screen.
Input / Output:
-i, --input-file FILE
Name of the multi-FASTA input file. Valid filetypes are: fa and fasta.
-o, --output-file FILE
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.
General Algorithm Parameters:
-m, --method METHOD
Select method to use. One of N2, D2, D2Star, and D2z. Default: N2.
-k, --k-mer-size K
Size of the k-mers. Default: 4.
-mo, --bg-model-order ORDER
Order of background Markov Model. Default: 1.
N2 Algorithm Parameters:
-rc, --reverse-complement MODE
Which strand to score. Use both_strands to score both strands simultaneously. One
of input, both_strands, mean, min, and max. Default: input.
-mm, --mismatches MISMATCHES
Number of mismatches, one of 0 and 1. When 1 is used, N2 uses the k-mer-neighbour
with one mismatch. Default: 0.
-mmw, --mismatch-weight WEIGHT
Real-valued weight of counts for words with mismatches. Default: 0.1.
-kwf, --k-mer-weights-file FILE.TXT
Print k-mer weights for every sequence to this file if given. Valid filetype is:
txt.
CONTACT AND REFERENCES
For questions or comments, contact:
Jonathan Goeke <goeke@molgen.mpg.de>
Please reference the following publication if you used ALF or the N2 method for
your analysis:
Jonathan Goeke, Marcel H. Schulz, Julia Lasserre, and Martin Vingron. Estimation of
Pairwise Sequence Similarity of Mammalian Enhancers with Word Neighbourhood Counts.
Bioinformatics (2012).
Project Homepage:
http://www.seqan.de/projects/alf
VERSION
alf version: 1.1 Last update January 5, 2012
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