SOWHAT

From MolEvol
Revision as of 14:50, 28 July 2015 by MarkHolder (talk | contribs) (Created page with "'''SOWHAT ?''' TEST 1 - CLASS DATA <code> cp -r /class/shared/SOWHAT_DEMO . cd SOWHAT_DEMO perl sowhat --aln=class_data.phy --constraint=other_hyp.tre --raxml_model=GTRGAMMA...")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)

SOWHAT ?

TEST 1 - CLASS DATA

cp -r /class/shared/SOWHAT_DEMO . cd SOWHAT_DEMO perl sowhat --aln=class_data.phy --constraint=other_hyp.tre --raxml_model=GTRGAMMA --dir=class_data --name=class --reps=200

      1. --aln = alignment file in PHYLIP sequential format
      2. --constraint = alternative hypothesis to be tested
      3. --raxml_model = model of evolution
      4. --dir = output directory
      5. --name = name of output files
      1. --reps = maximum simulated samples to generate
      2. * this is optional in real analysis *
      1. results printed to class_data/sowhat.results
      2. results are continuously printed after 10 samples
      3. and p-values / confidence intervals are
      4. calculated after each sample
      1. what does this p-value indicate about our alternative hypothesis?
      2. after how many samples did the conf. intervals show sufficient sampling?
                1. TEST 2 - MORE DATA #####

sowhat --aln=game_simul.phy --constraint=other_hyp.tre --raxml_model=GTRGAMMA --dir=game_sim --name=game --reps=200

      1. results printed to game_sim/sowhat.results
      1. how do the results of this test compare to the previous?
                1. FILES #######################
        1. class_data.phy = sequences generated from our game
        2. number of taxa = 4, number of sites = 27
        1. game_simul.phy = longer sequences generated using game parameters
        2. number of taxa = 4, number of sites = 1000
        1. other_hyp.tre = tree incongruent with ML tree
        2. internal node has been "flipped"