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. Author manuscript; available in PMC: 2021 Jan 18.
Published in final edited form as: Methods Mol Biol. 2021 Jan 1;2231:203–224. doi: 10.1007/978-1-0716-1036-7_13

Table 1. File formats supported by Jalview.

Format Extension Sequence Features Annotation Import only Notes
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