alf1
Alignment free sequence comparison
Usage
alf [OPTIONS]
-i
IN.FASTA
[-o
OUT.TXT]
Overview
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 -
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: .sam[.*], .raw[.*], .gbk[.*], .frn[.*], .fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*], .fa[.*], .embl[.*], and .bam, where * is any of the following extensions: gz, bz2, and bgzf for transparent (de)compression.
-
-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 <[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
Releases
6 releases since Debian 8 (Jessie); the text changed 2 times.
--bg-model-order since Debian 10 (Buster);
--help since Debian 10 (Buster);
--input-file since Debian 10 (Buster);
--k-mer-size since Debian 10 (Buster);
--k-mer-weights-file since Debian 10 (Buster);
--method since Debian 10 (Buster);
--mismatch-weight since Debian 10 (Buster);
--mismatches since Debian 10 (Buster);
--output-file since Debian 10 (Buster);
--reverse-complement since Debian 10 (Buster);
--verbose since Debian 10 (Buster);
--version since Debian 10 (Buster);
-h since Debian 10 (Buster);
-i since Debian 10 (Buster);
-k since Debian 10 (Buster);
-kwf since Debian 10 (Buster);
-m since Debian 10 (Buster);
-mm since Debian 10 (Buster);
-mmw since Debian 10 (Buster);
-mo since Debian 10 (Buster);
-o since Debian 10 (Buster);
-rc since Debian 10 (Buster);
-v since Debian 10 (Buster).