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Chapter and Conference Paper
Aligning Two Genomic Sequences That Contain Duplications
It is difficult to properly align genomic sequences that contain intra-species duplications. With this goal in mind, we have developed a tool, called TOAST (two-way orthologous alignment selection tool), for p...
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Chapter and Conference Paper
Controlling Size When Aligning Multiple Genomic Sequences with Duplications
For a genomic region containing a tandem gene cluster, a proper set of alignments needs to align only orthologous segments, i.e., those separated by a speciation event. Otherwise, methods for finding regions u...