#-------------------------------------------------------------------------------
# Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
# Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
#
# This file is part of Jalview.
#
# Jalview is free software: you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
#
# Jalview is distributed in the hope that it will be useful, but
# WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR
# PURPOSE. See the GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along with Jalview. If not, see .
#-------------------------------------------------------------------------------
Pairwise Alignment
Pairwise alignment (Proteins only)
This calculation is performed on the selected sequences only. Java is not the
fastest language in the world and aligning more than a handful of sequences
will take a fair amount of time.
For each pair of sequences the best global alignment is found using BLOSUM62
as the scoring matrix. The scores reported are the raw scores. The sequences
are aligned using a dynamic programming technique and using the following gap
penalties :
Gap open : 12
Gap extend : 2
When you select the pairwise alignment option a new window will come up which
will display the alignments in a text format as they are calculated. Also displayed
is information about the alignment such as alignment score, length and percentage
identity between the sequences.