Difference between revisions of "SOWHAT"

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(TEST 1 - CLASS DATA)
 
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== TEST 1 - CLASS DATA ==
 
== TEST 1 - CLASS DATA ==
  
<code>cp -r /class/shared/SOWHAT_DEMO .</code><br />
+
<code>module load bioware
 +
 
 +
cp -r /class/shared/SOWHAT_DEMO .</code><br />
 +
 
 
<code>cd SOWHAT_DEMO</code><br />
 
<code>cd SOWHAT_DEMO</code><br />
 +
 
<code>./sowhat --aln=class_data.phy --constraint=other_hyp.tre --raxml_model=GTRGAMMA --dir=class_data --name=class --reps=200</code><br />
 
<code>./sowhat --aln=class_data.phy --constraint=other_hyp.tre --raxml_model=GTRGAMMA --dir=class_data --name=class --reps=200</code><br />
  
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p-values  &  confidence intervals are  
 
p-values  &  confidence intervals are  
 
calculated after each sample
 
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?
 
What does this p-value indicate about our alternative hypothesis?
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== FILES ==
 
== FILES ==
  
class_data.phy = sequences generated from our game
+
class_data.phy = sequences generated from our game -
 
number of taxa = 4, number of sites = 27
 
number of taxa = 4, number of sites = 27
  
game_simul.phy = longer sequences generated using game parameters
+
game_simul.phy = longer sequences generated using game parameters -
 
number of taxa = 4, number of sites = 1000
 
number of taxa = 4, number of sites = 1000
  
 
other_hyp.tre  = tree incongruent with ML tree - internal node has been "flipped"
 
other_hyp.tre  = tree incongruent with ML tree - internal node has been "flipped"

Latest revision as of 20:49, 28 July 2015

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"