Difference between revisions of "SOWHAT"

From MolEvol
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'''SOWHAT ?'''
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== SOWHAT ? ==
  
 
TEST 1 - CLASS DATA
 
TEST 1 - CLASS DATA
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--reps = maximum simulated samples to generate * this is optional in real analysis *
 
--reps = maximum simulated samples to generate * this is optional in real analysis *
  
''results printed to class_data/sowhat.results''
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Results printed to class_data/sowhat.results
 +
 
 
Results are continuously printed after 10 samples
 
Results are continuously printed after 10 samples
 
and p-values /  confidence intervals are  
 
and p-values /  confidence intervals are  
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After how many samples did the conf. intervals show sufficient sampling?
 
After how many samples did the conf. intervals show sufficient sampling?
  
######## TEST 2 - MORE DATA #####
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== TEST 2 - MORE DATA ==
  
sowhat --aln=game_simul.phy --constraint=other_hyp.tre --raxml_model=GTRGAMMA --dir=game_sim --name=game --reps=200
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<code>sowhat --aln=game_simul.phy --constraint=other_hyp.tre --raxml_model=GTRGAMMA --dir=game_sim --name=game --reps=200</code>
  
### results printed to game_sim/sowhat.results
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results printed to game_sim/sowhat.results
  
### how do the results of this test compare to the previous?
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how do the results of this test compare to the previous?
  
######## FILES #######################
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== FILES ==
  
#### class_data.phy = sequences generated from our game
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class_data.phy = sequences generated from our game
#### number of taxa = 4, number of sites = 27
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number of taxa = 4, number of sites = 27
  
#### game_simul.phy = longer sequences generated using game parameters
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game_simul.phy = longer sequences generated using game parameters
#### number of taxa = 4, number of sites = 1000
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number of taxa = 4, number of sites = 1000
  
#### other_hyp.tre  = tree incongruent with ML tree
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other_hyp.tre  = tree incongruent with ML tree
####                internal node has been "flipped"
+
                internal node has been "flipped"

Revision as of 14:54, 28 July 2015

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?

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"