#-------------------------------------------------------------------------------
# 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
Alignment Fileformats
Jalview understands a wide range of sequence alignment formats. In order to determine which format has been used for an alignment, jalview tries to detect some text or formatting unique to one of the formats:
Format | Unique File Feature | File Extension |
FASTA | >SequenceName THISISASEQENCE |
.fa, .fasta |
MSF | !! AA_MULTIPLE_ALIGNMENT 1.0 .. // |
.msf |
CLUSTALW | CLUSTAL | .aln |
PILEUP | PileUp | |
PIR | >P1; | .pir |
BLC | >Seq1 >Seq2 |
.blc |
PFAM | SequenceName THISISASEQENCE | .pfam |
The file extensions are used to associate jalview alignment icons with alignment files: