Whole genome alignment

Several tools exist for alignment of whole genomes. They may be tuned for different target sequence distances.

• WABA
• BLASTZ -> LASTZ
• LAGAN and MLAGAN
• MUMMER
• AVID
• MAUVE
• Mercator

Finding nearly identical regions in whole genomes very fast

• BLAT
• SSAHA
• BLAST (megablast)