NAME¶

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.

OPTIONS

-h, --help

Display the help message.

--version-check BOOL

Turn this option off to disable version update notifications of the application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO. Default: 1.

--version

Display version information.

-v, --verbose

When given, details about the progress are printed to the screen.

Input / Output:

-i, --input-file INPUT_FILE

Name of the multi-FASTA input file. Valid filetypes are: .fasta and .fa.

-o, --output-file OUTPUT_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[.*], where * is any of the following extensions: tsv for transparent (de)compression.

General Algorithm Parameters:

-m, --method STRING

Select method to use. One of N2, D2, D2Star, and D2z. Default: N2.

-k, --k-mer-size INTEGER

Size of the k-mers. Default: 4.

-mo, --bg-model-order INTEGER

Order of background Markov Model. Default: 1.

N2 Algorithm Parameters:

-rc, --reverse-complement STRING

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 INTEGER

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 DOUBLE

Real-valued weight of counts for words with mismatches. Default: 0.1.

-kwf, --k-mer-weights-file OUTPUT_FILE

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

Last update: alf version: 1.1.8 [tarball] SeqAn version: 2.3.1