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SeqanTcoffee

SeqAn::T-Coffee is a multiple sequence alignment tool.

Web Documentation for SeqanTcoffee

Options

version-check: Turn this option off to disable version update notifications of the application.
alphabet: The used sequence alphabet.
method: Defines the generation method for matches. To select multiple generation methods recall this option with different arguments.
pairwise-alignment: Pairwise alignment method. Default: unbanded for usual alignments (< 50 sequences), banded for deep alignments (>= 50 sequences)
band-width: Band width. This option automatically select banded pairwise alignment (see pa for details)
gop: gap open penalty
gex: gap extension penalty
matrix: score matrix
msc: match score
mmsc: mismatch penalty
usetree: Name of the file containing the Newick Guide Tree.
build: Method to build the tree. Following methods are provided: Neighbor-Joining (nj), UPGMA single linkage (min), UPGMA complete linkage (max), UPGMA average linkage (avg), UPGMA weighted average linkage (wavg). Neighbor-Joining creates an unrooted tree, which we root at the last joined pair.

Input Ports

: Name of multi-fasta input file. [fa,fasta,faa,ffn,fna,frn,opt.]
: Name of match file. To select multiple files recall this option with different arguments. [blast,mums,aln,lib,opt.]
: Name of the alignment file <FASTA FILE> [fa,fasta,faa,ffn,fna,frn,opt.]

Output Ports

: Name of the output file. [fa,fasta,faa,ffn,fna,frn,msf]

Popular Predecessors

Popular Successors

Views

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

Workflows

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: 2024-12-23

KNIME versions: From v3.6 to v4.7

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