Upload files in Jalview

Hello,

Currently is possible change the parameters of the execution of an alignment, for example, choose the substitution matrix. it is possible uploading an matrix (or other file) in Web Service → Alignment → edit settings and run?

Hello again, Laécio.

Currently is possible change the parameters of the execution of an alignment, for example, choose the substitution matrix. it is possible uploading an matrix (or other file) in Web Service -> Alignment -> edit settings and run?

Unfortunately, no. Alignment settings such as the substitution matrix parameter are defined by the service interface for the JABAWS server that Jalview is connected to.

From your emails over at jabaws-discuss I gather you have set up your own JABAWS server - which means you could configure these settings on the server to allow custom substitution matrices, but they would have to be provided server-side rather than client side. Alternatively, you could consider creating a new MSA service interface that can take - in addition to sequences and parameters, a substitution matrix file. However, you'd then have to extend the existing JABAWS client library (and Jalview) in order to to allow Jalview to use the new interface.

Happy to talk more about this if you are interested in proceeding !
Jim.

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On 09/03/2015 03:26, Laécio Freitas Chaves wrote:

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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, College of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
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