X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2Fio%2Ffileformats.html;h=d887f1870472afd1faf1dc203c716f89ed5f74a9;hb=3a5e7da51af0166273109f98bdf942e733105233;hp=797a7c485ae1fad96fe9a8c89f8b2854892bda25;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html index 797a7c4..d887f18 100755 --- a/help/html/io/fileformats.html +++ b/help/html/io/fileformats.html @@ -1,64 +1,110 @@ +
+Alignment Fileformats -
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 -THISISASEQENCE |
-.fa, .fasta | -
MSF | -!! AA_MULTIPLE_ALIGNMENT 1.0 -.. -// |
-.msf | -
CLUSTALW | -CLUSTAL | -.aln | -
PILEUP | -PileUp | -- |
PIR | ->P1; | -.pir | -
BLC | ->Seq1 ->Seq2 |
-.blc | -
PFAM | -SequenceName THISISASEQENCE | -.pfam | -
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: +