SAP: News and Downloads

A bug I accidentally introduced in the 1.0.5 version was removed. This caused the homology set compilation against GenBank to fail. I also added better error handling for the GUI and a few other minor fixes.

As WU-blast is no longer available as free-ware SAP now uses NCBI blast instead. SAP will install it for you if you try to use a local database. Also fixed a number of reported bugs related to use of local databases.

Fixed a bug in force including of homologues, and a bug that made the constraint generation in Barcoder crash.

If your sequence is from one of loci used in the Barcode of Life Initiative (BOLI), e.g. cytochromoxidase I, you can make use of the fact that the sequences in GenBank that have been curated by the standards set by BOLI are associated with the keywork "barcode". If you use the limit query on the blast searches like this:

sap -d myproject --limitquery barcode[keyword] mysequence.fasta

then SAP will only consider this smaller more reliable subset in your analysis.

Precompiled statistics for the assignment step was not deleted correctly when a re-analysis in an existing project was run with different parameters for homology set compilation. A bug in the compilation of a local database from a fasta file was also fixed and the automatic installation of netblast was tweaked to work better.

After restructuring the code a typo made the GUI crash. Sorry about that. Here is the version with the bug fixed:

The rights to WU-BLAST have being acquired by Advanced Biocomputing, LLC. For that reason it is not available at the moment. When it will be, and at what price, I don't know. This obviously presents a problem to SAP users that want to use a locally formatted database. I will make SAP able to use (the inferior) NCBI blast to aid SAP users without wu-blast.

The official 1.0 version is now available for download. Beware: The names of some options have been changed to more suitable names. In addition the package now supports the use of a local database. For this to work you need wu-blast installed on your system. See the manual pages for information on how to format the your database file. Still I it is grately appreciated if you report any problems you come across with the package.

Command line version

Graphical user interface

The package has been tested thoroughly though use in a variety of data analyses. However, this is still the first official release of SAP so if you come across any problems you can help yourself and future users by reporting them.

Unfortunately the MCMC tree sampling is currently broken in the Windows version of SAP. However using the option '—sampling ConstrainedNJ' you can sample trees using constrained neighbour joining + bootstrapping. I hope to resolve this problem soon.

Command line version

Graphical user interface