Open mickvv opened 9 months ago
Maybe you called phymltest()
twice? See ?unique.multiPhylo
to try to check this.
Cheers, Emmanuel
Thank you for your quick answer.
I run this command:
phyml.sylvia <- phymltest("sylvia.phy", execname="/usr/bin/phyml")
I've tried removing the _phyml_tree.txt
output to avoid appending to the same file.
Thanks for the ?unique.multiPhylo
, it is a useful command but in my case I go from 56 to 11 trees.
I also looked at the _phyml_stats.txt
and there are indeed 28 runs listed.
It seems that for each model tested, 2 trees are produced but I don't know which one to choose out of the 56...
My goal is to get the tree for the best model.
Cheers, Mick
It seems like a bug in phyml. Using sequence data from here, the (shell) command:
phyml -i sylvia.txt
runs fine and creates the file 'sylvia.txt_phyml_tree.txt' with a single tree. Then if I run:
phyml -i sylvia.txt --append
the file has 3 trees (or 2 if I delete the output files beforehand).
I'm adding @stephaneguindon to this thread.
This is under Ubuntu (for me).
@mickvv Since each tree is duplicated, you should be able to get one tree out of two with:
TR <- read.tree("sylvia.phy_phyml_tree.txt") # using changed file extension
TR[c(TRUE, FALSE)]
Also, the next one should give you the same 28 trees:
unique.multiPhylo(TR, use.edge.length = TRUE)
Cheers, Emmanuel
Just checked my version number of phyml (under Ubuntu 22):
3:3.3.20211231-1
Thank you very much, I think it will do the trick !
Regards, Mick
It seems like a bug in phyml. Using sequence data from here, the (shell) command:
phyml -i sylvia.txt
runs fine and creates the file 'sylvia.txt_phyml_tree.txt' with a single tree. Then if I run:
phyml -i sylvia.txt --append
the file has 3 trees (or 2 if I delete the output files beforehand).
I'm adding @stephaneguindon to this thread.
This is under Ubuntu (for me).
@mickvv Since each tree is duplicated, you should be able to get one tree out of two with:
TR <- read.tree("sylvia.phy_phyml_tree.txt") # using changed file extension TR[c(TRUE, FALSE)]
Also, the next one should give you the same 28 trees:
unique.multiPhylo(TR, use.edge.length = TRUE)
Cheers, Emmanuel
Thanks. I will take a look at this issue. Regards, -Stephane-
When running phymltest() with the 28 models, the produced treefile _phyml_tree.txt contains 56 trees instead of expected 28.
Is it normal ?
Thanks Mick