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  • What is a gene family in PhyloGenes?
  • How is the boundary of a gene family defined?
  • What is the procedure you used in building a gene family and constructing its gene tree?
  • How are PANTHER gene trees constructed?
  • How is branch length calculated?
  • Why aren’t there any bootstrap or other support values for the tree topology?
  • What is a subfamily?
  • How are gene families named? Why are some families not named?
  • How are subfamilies named. Why are some subfamilies not named?
  • What is horizontal gene transfer? How is it detected in PANTHER gene trees?
  • Are polyploid organisms represented in gene families?
  • How does tree pruning work? Does pruning change the tree topology?

  • My gene is not found in PhyloGenes. Why?


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