| AMSA |
.amsa |
✔ |
|
✔ |
✔ |
|
| FASTA |
.fa, .fasta |
✔ |
|
|
|
Jalview does not currently support “FASTQ” style quality data embedded in FASTA records |
| Block |
.blc |
✔ |
|
✔ |
|
Header lines are available via the “Alignment Properties” dialog. For BLC files produced by an iterative search program such as ScanPS, the first iteration is loaded by default. A specific iteration can be retrieved by appending the filename with “#2” (to retrieve iteration 2) |
| Clustal |
.aln |
✔ |
|
|
|
The “Clustal” version header in files written by Jalview is hard coded, which may cause compatibility problems with other programs that require a specific version header |
| MSF |
.pileup, .aln |
✔ |
|
|
|
|
| Protein Information Record |
.pir |
✔ |
|
✔ |
|
Jalview supports MODELLER [22] style PIR description lines [23] to specify the filename and chain in a PDB [24] or mmCIF [25] file that maps to a sequence |
| Phylip |
|
✔ |
|
|
|
|
| Pfam |
.pfam |
✔ |
|
|
|
|
| Stockholm |
.stk, .stockholm |
✔ |
✔ |
✔ |
|
In addition to sequence, features, and annotation, Jalview also imports any provided database cross-references for a sequence (including PDB [24] database identifiers) and generic annotation tags associated with the alignment |
| Jalview Features Format |
.jvfeats |
|
✔ |
|
|
|
| T-COFFEE Score file |
.score_ascii |
|
|
✔ |
|
Jalview will raise an error if the number of sequences and columns in the score file does not match the alignment |
| Jalview Annotations Format |
.jvannot |
|
|
✔ |
|
|
| Generic Features Format (V3) |
.gff, .gff2, .gff3 |
✔ |
✔ |
|
|
|
| Variant Call Format (indexed) |
.vcf, .vcf.tbi |
|
✔ |
|
|
A protein or DNA contig with chromosomal coordinates must first be loaded before it can be annotated with variants from VCF files |
| BioJSON |
.json, biojson, html |
✔ |
✔ |
✔ |
|
A JSON hash containing elements structured according to BioJSON scheme can also store Groups, color schemes, Hidden columns, and sequences. Jalview will also search HTML files for embedded BioJSON |
| Jalview Project |
.jvp, .jar |
✔ |
✔ |
✔ |
|
Projects preserve all aspects of a Jalview session, including the layout of windows showing alignments, trees, and 3D structures |
| PDB |
.pdb, .ent |
✔ |
✔ |
✔ |
* |
Only 3D structures imported as PDB [24] files can be exported as PDB files |
| mmCIF |
.mmcif, .cif |
✔ |
✔ |
✔ |
* |
Only 3D structures imported as mmCIF files can be exported as mmCIF files |
| Newick |
.tree, ,nw |
|
|
|
* |
Jalview supports both simple Newick [26] and Extended Newick [27] and will preserve distances and bootstrap values detected in the file. It only exports trees in simple Newick format |
