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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:

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: