Deleted:Results changing using ete3
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7 weeks ago
mnsp088 ▴ 60

Hi all,

I'm running ete3 evol to detect positive selection in a list of orthologs. I realized something strange, I get different results if I run with lots of orthologs vs. just a couple. This is strange because I'm running it using a bash loop and so each ortholog/iteration should be independent of each other.

Here is my code:

for i in $(ls); do cd $i echo $i ete3 evol -t clustalo_default-none-none-fasttree_full/$i.fa.final_tree.nw --alg clustalo_default-none-none-fasttree_full/$i.fa.final_tree.used_alg.fa
-o paml_results/ --models M1 M2 --image figure.pdf cd .. done

and here is an example of how the results change..If i run ortholog_X in a loop with 2 other orthologs I get:

Positively selected sites

         Prob(w>1)      mean w

86 M      0.969*        5.961 +- 2.623

When I run ortholog_X in a loop with ~1K other orthologs I get:

Positively selected sites

         Prob(w>1)       mean w

86 M      0.996**       7.194 +- 2.259

Results seem to be more significant if you run the loop with more iterations. Anyone have any ideas why this would happen?

selection ete3 paml • 108 views
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