User:R. Eric Collins/MBL/Alignment

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Alignment Lab

  • Guide Trees:
    • Over-use of guide tree can cause circularity
  • Amino acid alignment back-convert to nucleotides
    • Mesquite
  • MEGA
    • EMBOSS
    • MAFFT in SeaView
  • Filtering:
    • There is a difference between highly certain but variable and highly uncertain and variable
    • GUIDANCE: throws out uncertain columns
    • GBLOCKS: throws out variable columns
  • Questions:
  1. Align short sequences to reference alignment
    • KC Dunlop?
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