Re: [R-sig-phylo] Can't load a tree with multitomies into 'ape'

Hi Liam, Thanks for explaining what is wrong with the format of the newick tree file. I will work in understanding and re-writing the tree with the correct formatting. Your script worked fine and the tree is finally in R! Thanks a lot. I appreciate your help Regards, Anna -Original Mess

Re: [R-sig-phylo] Can't load a tree with multitomies into 'ape'

Great, François. Now I have the tree in R and can continue with the next steps. Thanks a lot for your help Anna From: François Michonneau [mailto:francois.michonn...@gmail.com] Sent: Freitag, 15. August 2014 16:07 To: Anna Bastian Cc: r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Can't

Re: [R-sig-phylo] Can't load a tree with multitomies into 'ape'

Hi Anna. Your attached file with extension .nwk is also a Nexus style file so it cannot be read with read.tree or read.newick. read.tree and read.newick read a simple Newick style text string, or a set of such strings on separate lines in a file. It looks like the problem with your Nexus fil

Re: [R-sig-phylo] Can't load a tree with multitomies into 'ape'

Hi Anna, I can read your tree using the package phylobase: tr <- readNexus(file="IndTree.nex") If you need it in the phylo format to use with other functions in ape, you can convert it with: as(tr, "phylo") cheers, -- François On Fri, Aug 15, 2014 at 9:56 AM, Anna Bastian wrote: >

[R-sig-phylo] Can't load a tree with multitomies into 'ape'

Dear list members, I am trying to read a tree into R ('ape' package). I downloaded the latest versions. The tree has many polytomies and that might be the problem. It contains ten species and each species contains of a different number of individuals (those are the polytomies). I attached it he