-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 info about Jalview JSON format |
-.json | -
The file extensions are used to associate jalview alignment icons
-with alignment files:
-
+ 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:
+