From 273c70da46cafab18b55ca35d3fc02971cf0f6f3 Mon Sep 17 00:00:00 2001 From: jprocter Date: Mon, 10 Apr 2006 13:10:43 +0000 Subject: [PATCH] added bit about modeller/pir --- help/html/io/index.html | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/help/html/io/index.html b/help/html/io/index.html index 79e7576..d57de42 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -3,7 +3,8 @@

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 @@ -34,7 +35,9 @@ 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. +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.

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