A PhD thesis on comparative genomics "METHODS FOR HIGH-THROUGHPUT COMPARATIVE GENOMICS AND DISTRIBUTED SEQUENCE ANALYSIS" @ http://drum.lib.umd.edu/bitstream/handle/1903/11669/Angiuoli_umd_0117E_12062.pdf;jsessionid=A30813F9A1A23A54D917BC34109FE38D?sequence=1
I found this PPT tutorial useful
http://schatzlab.cshl.edu/teaching/AssemblyClass/06.%20Whole%20Genome%20Alignment.pdf