blast2tree

Blast2tree 1.0 assists in the identification of DNA sequences from microorganisms by sending automated queries to the NCBI BLAST and GenBank databases.

In response to a sequence query, the BLAST server returns a set of similar sequences; additional information, including sequence origin and bibliographic information is retrieved from GenBank. Results from both queries are aggregated and stored for subsequent analysis. The user can then select a subset of sequences to display in a spreadsheet and include in a multiple sequence alignment and phylogenetic tree. Sequences may be filtered based on name, number of ambiguities, presence of a corresponding peer reviewed publication, length, etc. Intended for use by medical technologists, the software is now part of the daily workflow fro the sequence-based identification of bacteria and fungi in the clinical laboratory.

Other software not available from the University of Washington that works with Blast2tree 1.0:

Clustalw is used to generate sequence alignments and phylogenetic trees.Thompson, J.D., Higgins, D.G. and Goibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alighmnets through sequence weighting, position specific gap penalties and weight matrix choice. Nucl. Acids Res. 22:4673-4680.

ReportLab Toolkit python package is used to generate pdf output.

Licensing Information

blast2tree is one of the many software programs and tools created at the University of Washington available through our Express Licensing Program. These agreements have standard terms and conditions that allow for rapid licensing by companies, organizations, or individuals

Academic License

License

This software is royalty-free to academic end-users based on a UW Free Fork license.

Commercial License

For licensing information for users at commercial companies, contact the Express Licensing Program.

The conditions and financial terms of this license apply only to those who download the license, sign it and return it "as is" to the UW Center for Commercialization. Some Express Licenses may be modified for an additional cost. Other licensing arrangements may be available.

For Descriptive and Technical Information

Noah Hoffman
Department of Laboratory Medicine
University of Washington Box 357110 1959 NE Pacific Street, NW120
Seattle, WA 98195-7110

Email: 

For Licensing Information/Customer Service

Express Licensing Program
UW Center for Commercialization
4311 11th Avenue NE, Suite 500
Seattle, WA 98105-4608
Phone: (206) 543-3970
Fax: (206) 616-3322
Email: license@u.washington.edu