SOWHAT

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Revision as of 18:53, 28 July 2015 by Schurch (talk | contribs)

SOWHAT ?

Code at https://github.com/josephryan/sowhat. Preprint at http://biorxiv.org/content/early/2015/05/07/005264

TEST 1 - CLASS DATA

module load bioware

cp -r /class/shared/SOWHAT_DEMO .
cd SOWHAT_DEMO
./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 analyses *


Results printed to class_data/sowhat.results

Results are continuously printed after 10 samples, p-values & confidence intervals are calculated after each sample


NOTE: If you need to rerun the analysis, delete the directory generated using --dir or attach the option --restart



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

After how many samples did the conf. intervals show sufficient sampling?

TEST 2 - MORE DATA

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

results printed to game_sim/sowhat.results

how do the results of this test compare to the previous?

FILES

class_data.phy = sequences generated from our game - number of taxa = 4, number of sites = 27

game_simul.phy = longer sequences generated using game parameters - number of taxa = 4, number of sites = 1000

other_hyp.tre = tree incongruent with ML tree - internal node has been "flipped"