Alignment File Formats
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 THISISASEQUENCE |
.fa, .fasta |
| MSF | !! AA_MULTIPLE_ALIGNMENT 1.0 .. // |
.msf |
| CLUSTALW | CLUSTAL | .aln |
| PILEUP | PileUp | |
| PIR | >P1; | .pir |
| BLC | >Seq1 >Seq2 |
.blc |
| PFAM | SequenceName THISISASEQUENCE | .pfam |
| Stockholm | # STOCKHOLM VersionNumber ... // |
.stk, .sto |
| Phylip | Line starts with two numbers separated by
white space ... // |
.phy |
| EMBL | Line starts with ID, followed by a space, and is followed by a 7 character identifier terminated with a semicolon. | .txt |
| GenBank | Line starts with LOCUS | .gb,.gbk |
| JSON | Data starts with '{' Data ends with '}' See BioJSON for more infomation about the Jalview JSON format |
.json |
The file extensions are used to associate Jalview alignment icons
with alignment files: