Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences.
Cinteny is a flexible and efficient tool for analysis of synteny and evolutionary distances in terms of genome rearrangements (the reversal distance) for multiple genomes. In addition to annotated genomes, which are available for interactive browsing and assessment of synteny and evolutionary distances in terms of orthologous genes, Cinteny can be used with user provided discrete objects, such as sequence tags or other evolutionarily conserved markers.
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