PAML notes

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For the lab

Log into the cluster

   module load bioware
   cd 2014_Paml_lab

Codon Alignments

This is not part of the exercises, it's just for your future information.

To run the analyses described here, you will need a codon alignment (i.e. a nucleotide alignment that, when translated, corresponds perfectly to a good amino acid alignment). You can't just align nucleotides because most alignment programs don't look for codons, so the program may put gap characters in the middle of codons, throwing the sequences out of frame. You have to align the amino acids, and then force your unaligned nucleotides to fit that alignment.

We have shown you how to translate the nucleotides in SeaView and align amino acids using MAFFT or Muscle, but not how to get back to codons. The Pal2Nal server is good for this. You will upload your protein alignment and nucleotide sequences, and it will spit out the codon alignment. Please be aware that your nucleotides must be multiples of three (i.e. a full open reading frame).