SeqanTcoffee

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

(c) Copyright 2009 by Tobias Rausch

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

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

Output Ports

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

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

Further Links

Developers

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