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Table 1 Whole genomes alignement methods in the literature

From: Bacterial syntenies: an exact approach with gene quorum

    edition operations   
Name nb genomes correspondence INV/TRANS DUPL DEL algorithm reference
GRIMM pairwise one-to-one yes yes yes minimise evolutionary distance [6]
CINTENY pairwise many-to-many yes yes yes minimise evolutionary distance [7]
UNO AND TAGIURA pairwise one-to-one yes no no find common intervals [8]
HEBER AND STOYE multiple one-to-one yes no no find common intervals [9]
DIDIER pairwise many-to-many yes yes no find common intervals [10]
GENE TEAMS multiple equivalence yes no yes divide and conquer [11]
HOMOLOGY TEAMS pairwise equivalence yes yes yes divide and conquer [12]
DOMAIN TEAMS multiple equivalence yes yes yes divide and conquer [13]
MCGS multiple equivalence yes yes yes divide and conquer [14]
MCPA GE pairwise equivalence yes yes yes divide and conquer [15]
MCMU SE C multiple equivalence yes yes yes divide and conquer [16]
C3PART multiple many-to-many yes yes yes partition the NAM [17]
FISH pairwise many-to-many local no yes dynamic programming [18]
DAGCHAINER pairwise many-to-many no no yes dynamic programming [19]
COLINEAR SCAN pairwise many-to-many no no yes dynamic programming [20]
SYNTENATOR multiple many-to-many no yes yes dynamic programming on POG [21]
CYNTENATOR multiple many-to-many no yes yes same + phylogeny [22]
ADHO RE pairwise many-to-many no tandem yes clustering [30]
I-ADHO RE multiple many-to-many no tandem yes greedy heuristic [26]
  1. Principal approaches for whole genomes alignment and the search for syntenies. Note that the real goal of GRIMM and CINTENY is to reconstruct evolutionary scenarios, the extraction of syntenies is only a by-product of those algorithms. Note also that DOMAIN TEAMS uses a protein domain granularity, whereas all other methods operate at the gene level. Among the multiple comparison tools, MCGS (and its extension MCMU SE C), SYNTENATOR (and its extension CYNTENATOR) and I-ADHO RE can handle (directly or indirectly) a gene quorum.