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
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: