Alf

Compute pairwise similarity of sequences using alignment-free methods in IN.FASTA and write out tab-delimited matrix with pairwise scores to OUT.TXT.

Web Documentation for Alf

Options

version-check
Turn this option off to disable version update notifications of the application.
verbose
When given, details about the progress are printed to the screen.
method
Select method to use.
k-mer-size
Size of the k-mers.
bg-model-order
Order of background Markov Model.
reverse-complement
Which strand to score. Use both_strands to score both strands simultaneously.
mismatches
Number of mismatches, one of 0 and 1. When 1 is used, N2 uses the k-mer-neighbour with one mismatch.
mismatch-weight
Real-valued weight of counts for words with mismatches.

Input Ports

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Name of the multi-FASTA input file. [fq,fastq,fa,fasta,faa,ffn,fna,frn,embl,gbk,raw,sam]

Output Ports

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Name of the file to which the tab-delimtied matrix with pairwise scores will be written to. Default is to write to stdout. [alf.tsv]
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Print k-mer weights for every sequence to this file if given. [txt]

Views

Alf Std Output
The text sent to standard out during the execution of Alf.
Alf Error Output
The text sent to standard error during the execution of Alf. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Workflows

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Further Links

Developers

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