Dear Mothur users,
I am currently analyzing a data set following the “Costello stool analysis” example and I would like to generate a tree based on unifrac metrics.Â
Although, PCA plots based on weighted and unweighted unifrac output turn out great I am struggling with the commands to generate a tree based on unifrac output.
In Costello’s example it says: “By the same token, the construction of dendrograms as described above using the tree.shared command could be done with output from the unifrac commands”
I was wondering if someone could give me some specific commands.
sorry for that bit of vagueness… try tree.shared(phylip=stool.final.tre1.unweighted.dist)
That sounds good! Unfortunately, I get a strange error message when executing that command.
_mothur > tree.shared(phylip=allmice.final.tre1.weighted.dist)
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||
t03_CE10 is not in your name file, please correct._
However, t03_CE10 is a sample name and not a sequence name...?
when I execute:
mothur > read.tree(tree=allmice.final.tre, name=allmice.final.names, group=allmice.final.picks.groups)
mothur > unifrac.weighted(distance=T, random=F)
mothur > pcoa(phylip=allmice.final.tre1.weighted.dist)
Output File Names:
Thanks for reporting this bug. It will be fixed in 1.13.0, releasing later this month. In the meantime, you can work around it by exiting out of mothur after you create the allmice.final.tre1.weighted.dist file and then restarting mothur to run tree.shared command.