X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Ffileformats.html;h=af4e2c40672efb031dcc8a72cc0af5098a4d7940;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=f1cf5dc7997f43c063938d9f32022face63a02a5;hpb=a9edbad08eca203164152905ecd4d734ce72ecf5;p=jalview.git
diff --git a/help/html/io/fileformats.html b/help/html/io/fileformats.html
index f1cf5dc..af4e2c4 100755
--- a/help/html/io/fileformats.html
+++ b/help/html/io/fileformats.html
@@ -31,61 +31,80 @@ td {
-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 |
-
+
+ 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: 
-
+
+
+ The file extensions are used to associate Jalview alignment icons
+ with alignment files:
+