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Best match graphs and reconciliation of gene trees with species trees.

Manuela GeißMarcos E González LaffitteAlitzel López SánchezDulce I ValdiviaMarc HellmuthMaribel Hernández RosalesPeter F Stadler
Published in: Journal of mathematical biology (2020)
A wide variety of problems in computational biology, most notably the assessment of orthology, are solved with the help of reciprocal best matches. Using an evolutionary definition of best matches that captures the intuition behind the concept we clarify rigorously the relationships between reciprocal best matches, orthology, and evolutionary events under the assumption of duplication/loss scenarios. We show that the orthology graph is a subgraph of the reciprocal best match graph (RBMG). We furthermore give conditions under which an RBMG that is a cograph identifies the correct orthlogy relation. Using computer simulations we find that most false positive orthology assignments can be identified as so-called good quartets-and thus corrected-in the absence of horizontal transfer. Horizontal transfer, however, may introduce also false-negative orthology assignments.
Keyphrases
  • genome wide
  • mental health
  • dna methylation
  • climate change
  • copy number
  • convolutional neural network
  • deep learning
  • molecular dynamics
  • gene expression
  • machine learning
  • electron transfer