PairAlign

The program allows one to align two sequences using dyamic programming alignment algorithms while tweaking various parameters.

Web Documentation for PairAlign

Options

version-check
Turn this option off to disable version update notifications of the application.
alphabet
Sequence alphabet.
method
DP alignment method: Needleman-Wunsch, Gotoh, Smith-Waterman, Longest Common Subsequence
gop
Gap open penalty.
gex
Gap extension penalty.
matrix
Score matrix.
msc
Match score.
mmsc
Mismatch penalty.
low
Lower diagonal.
high
Upper diagonal.
config
Alignment configuration.

Input Ports

Icon
FASTA file with two sequences. [fa,fasta,faa,ffn,fna,frn]

Output Ports

Icon
Output filename. [fa,fasta,faa,ffn,fna,frn,msf]

Views

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

Workflows

Links

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.