OrthoAlign is a software for the gene order alignment problem (alignment of orthologs), accounting for most genome-wide evolutionary events such as duplications, losses, rearrangements and substitutions.
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Mol Biol Evol. 2015 Feb 6. pii: msv029.
Evolution of tRNA Repertoires in Bacillus Inferred with OrthoAlign.
Tremblay-Savard O, Benzaid B, Lang BF, El-Mabrouk N