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References for alignment programs

When using the JGI Alignment Search tool, you select an alignment program from one of three families of sequence alignment algorithms, BLAST, BLASTZ, or BLAT.

For general information about these tools and the parameters that govern their use (which you can set in the Program Settings panel ), please consult:

• NCBI Blast
• The UCSC Blastz genomewiki page
• The UCSC Blat FAQ

On the Alignment Results Page , in both the Hit Table and in Hit Graphs, you have the opportunity to view and download the raw output of these programs. You can find information about these formats here:

• Raw BLAST Output
• Raw BLAT Output (PSL/PSLX)
• Raw BLASTZ Output