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
Stockholm | # STOCKHOLM VersionNumber ... // | .stk, .sto

The file extensions are used to associate jalview alignment icons with alignment files: