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CarineRey / pcoc

Convergent substitution detection tool based on the PCOC model
GNU General Public License v3.0
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Question about pcoc usage #6

Closed Vizueta closed 6 years ago

Vizueta commented 6 years ago

Hello,

I write these issue as I am having some doubts and errors using pcoc. Basically, I would like to know if it makes sense to apply your method to a phylogenetic tree with only 5 species, in which only two branches are candidates to accumulate convergent changes (two events, see tree below)

(1,((2,3), (4.5))); # branches 2 and 5 are the candidates.

I ran your program with this configuration in 22 candidate genes from our previous genomic analysis and I got some sites with PP>0.95, but I am not sure if they are false positives.

In fact, I tried running a simulation study to answer this question. I used this command:

$CMD_PCOC_DOCKER pcoc_sim.py -t protein_aln/species_tree/ -o pcoc_sim/sptree_pcoc_det_sim -m "2/5" -c 2 -n_sc 1 --pcoc -nb_sampled_couple 10 -n_sites 100

Nevertheless, I got an error (see attached the output folder) and I don't know how to proceed. I used "/" to separate the scenarios, considering them as independent in each of these two branches, but I am not sure if I should use the comma instead, because results are not what I expect. OG6704_pcoc_det_sim_error.zip

I would greatly appreciate your help. Sincerely, Joel Vizueta.

CarineRey commented 6 years ago

Hello,

In fact it was a bug, I fixed it. Thank you for the report. Don't forget to do a docker pull carinerey/pcoc

Sincerely, Carine Rey