Re: from the very beginning

[Will]

Hello,

Thanks for getting in touch. It does sound like there might be something weird with how you've saved your file; I have received similar emails from people with the same problem.

Your input file should be in the same format as the demo files that come with phyloGenerator. Normally, that means a file saved from Excel is fine, but this would not be the first time that Excel did something weird to data! If you send me a copy of the species for you're using (to me, preferably, not the list) I will have a look at it for you.

Thanks again, and I hope I can help!

[Will]

Hello,

Good news! I've fixed the species file (and emailed the corrected version to you), and I've also made the phylogeny/constraint tree for you using my new R package pez, which contains some pG functions in it. I describe both below in case it's of use to other people.

The weird output is because your file was saved in a file encoding I've not seen before. phyloGenerator (or, more precisely, Python) was getting confused by the different way your file told the computer what characters were in your file. This has come up for others before: I just saved it as a UTF-8 file and it was all fine. If you use the emacs text editor, like me, type 'C-x C-m f' otherwise I'm sure there's an option in 'save as' to alter your encoding.

(You're trying to build a very large phylogeny, and so) I would recommend you use some kind of constraint tree if you can. Here is a way to build one very easily using pez in R:

#Load pez package

require(pez)

#Load phylogeny and species

tree <- read.tree("Vascular_Plants_rooted.dated.tre")

species <- read.delim("all.species.names.largedb.txt", as.is=TRUE)[,1]

#Make tree and drop unwanted species

tree <- congeneric.merge(tree, species)

tree <- drop.tip(tree, setdiff(tree$tip.label, species))

...for this I assume you have the phylogeny from Zanne et al. (2014) on your hard-drive somewhere. Note that, in this case, you've got ~550 species (of ~560) in your phylogeny now. So you can either use this as a constraint, or... just go ahead and use it as a tree for whatever you're doing. pez is simply running the merge/replace option in pG on the Zanne tree.

Let me know how you get on,

Will