6.891 Laboratory 2 Tools

  1. Knoppix Molevolution CD-rom (PC’s only so far, sorry): boot from CD (using Bios). Contains: ClustalX, TreeView, PAML, LAMARC, PAUP*, others.
  1. For dN/dS calculations
    1. SNAP
    2. (optional on PC): download DnaSP
  1. For alignments/format conversion: ClustalX
    1. Download for Mac 
    2. For PC, use Molix Cd-rom: clustalx
    3. (or download yourself on PC)
    4. General ClustalX web page
  1. For advanced dN/dS analysis using likelihoods, or PAML
    1. Download for Mac

See instructions/docs.

    1. For PC, use  Molix Cd-rom, codeml
    2. Or download .exe file for PC
  1. For Josh Plotkin’s volatility analysis      
    1. Codon Volatility Computation Server site
  1. For coalescent animation/tests, see:

Coalescent.dk web page  and click on “Wright-Fisher” animator or “Hudson” animator

  1. For drawing phyogenetic trees after alignment: use TreeView from the Cd-rom: tv

Data sources

  1. genes.tar.gz (TAR - 11 MB) -Yeast alignments
  2. chr2.tar.gz (TAR) - all alignments from chromosome 2
  3. Yeast database at Broad Institute.
  4. Test data for ‘warmup’ sections of the lab: The laboratory will include links to these files. (Kreitman drosophila data; human/primate globin data, etc.)