Difference between revisions of "SOWHAT"

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(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...")
 
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<code>
 
<code>
cp -r /class/shared/SOWHAT_DEMO .
+
cp -r /class/shared/SOWHAT_DEMO .</code><br />
cd SOWHAT_DEMO
+
cd SOWHAT_DEMO</code><br />
perl sowhat --aln=class_data.phy --constraint=other_hyp.tre --raxml_model=GTRGAMMA --dir=class_data --name=class --reps=200
+
perl sowhat --aln=class_data.phy --constraint=other_hyp.tre --raxml_model=GTRGAMMA --dir=class_data --name=class --reps=200</code><br />
</code>
 
  
### --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
+
--aln = alignment file in PHYLIP sequential format
###          * this is optional in real analysis *
 
  
### results printed to class_data/sowhat.results
+
--constraint = alternative hypothesis to be tested
###      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?
+
--raxml_model = model of evolution
### after how many samples did the conf. intervals show sufficient sampling?
+
 
 +
--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 #####
 
######## TEST 2 - MORE DATA #####

Revision as of 14:52, 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?

                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"