I am wondering if anyone recommend me better WGA tools available currently for aligning plant genomes. I am now using
Mauve, Mummer and Mugsy. Are there any better tools available?
Many people recommend Mauve or Mummer.
See also this link:
"Two types of pairwise genome alignment are available in Ensembl Genomes, based on LastZ  (or its predecessor BlastZ ) and translated BLAT (tBLAT) . LastZ is typically used for closely related species, and tBLAT for more distant species. The method of alignment affects the coverage of the genomes, with tBLAT expected to mostly find homologies in coding regions".
Vista is quite a good tool specially geared towards WGD in plants. WGDs can be downloaded or computed
PlantRegMap (http://plantregmap.cbi.pku.edu.cn) contains 644 pairwise genome alignments and 63 multiple genome alignments for 63 plants.
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