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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

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

Output Ports

: 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]
: Print k-mer weights for every sequence to this file if given. [txt]

Popular Predecessors

Popular Successors

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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Developers

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Installation

To use this node in KNIME, install the extension SeqAn from the below update site following our NodePit Product and Node Installation Guide:

v4.7

A zipped version of the software site can be downloaded here.

Plugin provider: Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Plugin version: 2.4.1.202004061533

On NodePit since: 2022-12-06

Last update: 2024-11-09

KNIME versions: From v3.6 to v4.7

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Alf