Man page - alf(1)
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- alf(1)
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- sak(1)
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- yara_mapper(1)
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- micro_razers(1)
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- seqan_tcoffee(1)
- pair_align(1)
- razers(1)
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Manual
| ALF(1) | ALF(1) |
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.
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 <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
| alf 1.1.10 [tarball] |