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alf - Online in the Cloud

Run alf in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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