X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Fio%2Findex.html;h=b0d6b043a1b5e2982ee958f74b7775c5864922aa;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=e18e273bc6e63d17a8266460e4a4915b193850f3;hpb=6ab4ef1cc71ff9d28a21a139db69e4a8351a3fb5;p=jalview.git diff --git a/help/html/io/index.html b/help/html/io/index.html index e18e273..b0d6b04 100755 --- a/help/html/io/index.html +++ b/help/html/io/index.html @@ -1,18 +1,101 @@ + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + --> + +Input/Output + + +

+ Input +

+

Jalview can read alignment files in any of the following + standard formats:

+

+ Fasta (Pearson), GCG-MSF, ALN/ClustalW, AMPS Block file, + NBRF/PIR (including MODELLER variant), Pfam/Stockholm +

+

+ Additionally, whole sets of coloured and annotated alignments and + trees can be read from a Jalview + (jar) format file using Desktop→Load + Project. +

+

+ Press "Control O" to open a file browser, or use the Desktop→Input + Alignment menu to read in alignments from: +

+ +

+ Jalview will try to recognise the file type automatically (using + some special features). If a file is + of an unknown format or there is any other error reading the + alignment file then you will be given an error message. If you think + Jalview really should be able to read your file, then send an email + containing the problem file to help@jalview.org. +

+

+ 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.
The project data includes the state of any open + structure viewers (Jmol, and since Jalview 2.9 also Chimera + and Varna). +

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