swMATH ID: 29670
Software Authors: Rödelsperger, C., Dieterich, C.
Description: CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes. Whole genome gene order evolution in higher eukaryotes was initially considered as a random process. Gene order conservation or conserved synteny was seen as a feature of common descent and did not imply the existence of functional constraints. This view had to be revised in the light of results from sequencing dozens of vertebrate genomes. It became apparent that other factors exist that constrain gene order in some genomic regions over long evolutionary time periods. Outside of these regions, genomes diverge more rapidly in terms of gene content and order. We have developed CYNTENATOR, a progressive gene order alignment software, to identify genomic regions of conserved synteny over a large set of diverging species. CYNTENATOR does not depend on nucleotide-level alignments and a priori homology assignment. Our software implements an improved scoring function that utilizes the underlying phylogeny. ..
Homepage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2812507/
Related Software: i-ADHoRe; Asgan; Sibelia; CAMSA; hybridSPAdes; GTED; HINGE; Canu; Bandage; Unicycler; AGB; PathRacer; Minimap2; dipSPAdes; SPAdes; iGTP; Triplet MaxCut; GASTS; ProCARs; ANGES
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