Man page - alf(1)
Packages contains this manual
- rabema_evaluate(1)
- alf(1)
- mason_materializer(1)
- pair_align(1)
- gustaf(1)
- stellar(1)
- razers3(1)
- sak(1)
- yara_indexer(1)
- mason_frag_sequencing(1)
- micro_razers(1)
- rabema_prepare_sam(1)
- insegt(1)
- rabema_build_gold_standard(1)
- splazers(1)
- seqan_tcoffee(1)
- yara_mapper(1)
- tree_recon(1)
- mason_genome(1)
- mason_methylation(1)
- razers(1)
- snp_store(1)
apt-get install seqan-apps
Manual
ALF
NAMESYNOPSIS
DESCRIPTION
OPTIONS
Input / Output:
General Algorithm Parameters:
N2 Algorithm Parameters:
CONTACT AND REFERENCES
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