X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Findex.html;h=d57de42e7adf719280f2be9a9fd8b98bb128cf33;hb=74fee91ef567d4637911a9c20834c9fb1de8c64a;hp=c521747058f81d4637bba05a666874616ea11300;hpb=5ee77e927b5f7fc838eddb22da954c7df11fcf53;p=jalview.git diff --git a/help/html/io/index.html b/help/html/io/index.html index c521747..d57de42 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -3,12 +3,14 @@
Input
Jalview can read alignment files in any of the following standard formats:
-Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm
+Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, +NBRF/PIR (including MODELLER variant), Pfam/Stockholm
The EBI has examples of these file formats.
Additionally, annotated whole sets of alignments and trees can be -read from a Jalview -(jar) format file using Desktop→Load Project.
+read from a Jalview (jar) +format file using Desktop→Load +Project.Use the Desktop→Input Alignment menu to read in files from:
Jalview can also read jalview specific files for sequence features +and alignment annotation.
Output
Each alignment, whether it is the original or an edited version may be saved in the standard formats using File→Save As
Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, NBRF/PIR, Pfam/Stockholm
+Jalview will by default append the sequence start and end to each sequence name, +in the format /start-end. If you do not want this behaviour for a particular file +output, open the "Output" tab on the Preferences window where you can +select which file formats you want to append the start and end sequence positions +for. In the case of PIR format, the output tab also contains a switch +for turning on the output of Modeller style structured description +lines. +Quantitative and symbolic alignment annotation can be exported as a +comma separated value file by right clicking on an annotation row +under the alignment.
You can also save the current set of alignments and their colours, annotations and trees in a Jalview archive file using Desktop→Save project.