SOWHAT

From MolEvol
Revision as of 14:52, 28 July 2015 by MarkHolder (talk | contribs)

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


--aln = alignment file in PHYLIP sequential format

--constraint = alternative hypothesis to be tested

--raxml_model = model of evolution

--dir = output directory

--name = name of output files


--reps = maximum simulated samples to generate * this is optional in real analysis *

results printed to class_data/sowhat.results Results are continuously printed after 10 samples and p-values / confidence intervals are calculated after each sample

What does this p-value indicate about our alternative hypothesis?

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"