This is the command alf that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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 <[email protected]>
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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