User:R. Eric Collins/MBL/Alignment

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?