6.891 Laboratory 2 Tools

  1. Knoppix Molevolution CD-rom (PCÕs only so far, sorry): boot from CD (using Bios). Contains: ClustalX, TreeView, PAML, LAMARC, PAUP*, others.
  2. For dN/dS calculations
    1. SNAP:  http://hcv.lanl.gov/content/hcv-db/SNAP/SNAP.html
    2. (optional on PC): download DnaSP from http://www.ub.es/dnasp/

 

  1. For alignments/format conversion: ClustalX
    1. Download for Mac from website: 

http://web.mit.edu.ezproxyberklee.flo.org/6.891/www/Clustalx-1.83-MacOS-X.tar

    1. For PC, use Molix Cd-rom: clustalx
    2. (or download yourself on PC): http://web.mit.edu.ezproxyberklee.flo.org/6.891/www/clustalx1.83.XP.zip
    3. General web page at : http://www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html
    4. For simple format conversions (fasta/clustalw/table/mega), if you donÕt want to use ClustalX, you can use the web form at:

http://hcv.lanl.gov/content/hcv-db/SEQCONVERT/seqconvert.html

 

  1. For advanced dN/dS analysis using likelihoods, or PAML
    1. Download for Mac from website: http://web.mit.edu/6.891/www/paml3.14.tar.gz

See instructions/docs at http://abacus.gene.ucl.ac.uk/software/paml.html

    1. For PC, use  Molix Cd-rom, codeml
    2. Or download .exe file for PC:  http://web.mit.edu/6.891/www/paml3.14.tar.gz

 

  1. For Josh PlotkinÕs volatility analysis 
    1. Server site: http://volatility.cgr.harvard.edu/cgi-bin/volatility.pl

 

  1. For coalescent animation/tests, see:

http://www.coalescent.dk/ and click on ÒWright-FisherÓ animator or ÒHudsonÓ animator

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

 

Data sources

  1. Yeast alignments downloadable directly http://web.mit.edu.ezproxyberklee.flo.org/6.891/www/genes.tar.gz  (11mb compressed, 64mb uncompressed; all alignments from chromosome 2: http://web.mit.edu.ezproxyberklee.flo.org/6.891/www/chr2.tar.gz  (813kb compressed, 9mb uncompressed)
  2. Yeast database at Broad Institute: http://www.broad.mit.edu.ezproxyberklee.flo.org/annotation/fungi/comp_yeasts/index.html
  3. Test data for ÔwarmupÕ sections of the lab: Kreitman drosophila data; human/primate globin data, etc. will all be on http://web.mit.edu.ezproxyberklee.flo.org/6.891/www/ as needed. (The laboratory will include links to these files)