The most easy way to use BlastViewer Tool consists in downloading an official release. It is made of a single Java binary archive file:

blastviewer-x.y.z.jar  (with 'x.y.z' being a release number, e.g. 5.5.0)

It is available from this Github page: check Releases tab and download the latest release.

We invite all users to start working with that "jar" file, as explained in the next section.

Notice for developers: this unique JAR file is absolutely not intended to be embedded within any other applications since it contains all the dependencies (third-party libraries) into a single large file. So, if you want to include BlastViewer into some other softwares, start from its source code (git clone).

Use a Java Virtual Machine 1.8 from Oracle. Do not use JRE 1.9 or above: for now, the UI framework (jGAF) used by BlastViewer is not compatible with recent JREs... work is in progress to fix that!

As a result of using Java, BlastViewer is available for Linux, macOS and Windows systems.

Not tested with any other JVM providers but Oracle... so there is no guarantee that the software will work as expected if not using Oracle's JVM.

After retrieving an official release of the BlastViewer software (see here), you can start it quite easily from a Terminal (Linux, Mac OSX and Windows):

java -jar blastviewer-5.5.0.jar

Windows, Mac OSX systems: you can also double click on the "jar" file to start the software.

BlastViewer is capable of reading legacy NCBI XML file. This is the result file you can create when using the following argument of BLAST :

-outfmt 5 

For those of you that are still using the legacy BLAST (i.e. blastall), use this argument:

-m 7

And for those of you that are using PLAST, use this argument:

-m 4

You can find sample BLAST XML files in the BlastViewer project, here. Use them to check your installation of BlastViewer.

BLAST XML file can be very huge. So, you could have to request the Java Virtual Machine to play with more memory using well known JVM arguments: -Xmx and -Xms.

For instance, the following command line starts BlastViewer with 256Mb of memory and will allow the process to use up to 4G of memory:

java -Xms256m -Xmx4G -jar blastviewer-5.5.0.jar

Starting with release 5.4.0, BlastViewer implements command-line arguments, as requested on issue #3.

Simply run the following command to review command-line options of BlastViewer:

java -jar blastviewer-5.4.0.jar -h

Arguments enable to open BLAST results from either files, URLs or NCBI Blast server (using job RIDs).

Examples:

java -jar blastviewer-5.4.0.jar -url "http://www.plealog.com/bv/blastp.xml"   (1)
java -jar blastviewer-5.4.0.jar -nrid HK740VV9016                             (2)
java -jar blastviewer-5.4.0.jar -in "../data/blastp.xml"                      (1)

Notes:

• (1) Use of double quotes is not mandatory but highly recommanded.
• (2) This example may not work anymore over time since NCBI jobs are stored on NCBI server with a time limit.

Arguments -in, -url and -nrid can be used several times simultaneously on a same commad-line, e.g.:

java -jar blastviewer-5.4.0.jar -url "http://www.plealog.com/bv/blastp.xml" -url "http://www.plealog.com/bv/p12253-refseq.xml"

Arguments -in, -url and -nrid are mutually exclusive, i.e. you cannot mix them in a same command-line.

Starting with BLAST Viewer release 5.5.0, it is possible to import data files produced by InterProScan. More here.