Bird species phylogenetic tree

[irene.torr...@gmail.com]

Hello,

It is the first time I do phylogenetic tree and above all, I'm interested in achieving a Newick or New Hampshire format tree file in order to use it to do a phylogenetic correlation matrix which in turn I want to introduce in a mixed effects model.

 

I’m using phyloGenerator: http://willpearse.github.io/phyloGenerator/guide.html

I proceeded in phyloGenerator till the DNA download step.  Then I had a lot of error messages regarding DTD files and warns about server errors. I let the program run but at the end it is blocked at a server error warn and nothing has happened for 2 hours.

My data:

-          I choose COI and vertebrates, as I’m analysing bird species

-          I introduced a .txt file with all my species listed in binomial form

-          My lists comprehends 139 species names, but there are some repeated ones (I’m doing a meta-analysis).

My questions:

-          How can I proceed?

-          How can I get a Newick or New Hampshire format tree files at the end?

Thanks a lot!

Irene

[Will]

Hello,

Thanks for getting in touch. I'm traveling right now, so I can only be brief, but:

1. Do not put the same species name twice into pG - this could lead to weird phylogenies. You shouldn't need to do that for any application, even a meta-analysis.
2. Try running it again. Server errors et al. are normally something to do with your Internet connection - just try one more time. DTD warnings can be safely ignored.
3. You'll get a Newick or a Nexus file out depending on the options you pick. Either can be loaded into R no problem - read.tree or read.nexus.

Let me know if this doesn't work for you - I might not get back to you until the weekend if there's very strange going on, but I will try!!!

Thanks again,

Will

[Will Pearse]

...which solved the problem, judging by an off-list conversation.

Cheers,

Will

On Wednesday, 27 January 2016 22:29:07 UTC-5, Will Pearse wrote:

Hello,

Thanks for getting in touch. I'm traveling right now, so I can only be brief, but:

1. Do not put the same species name twice into pG - this could lead to weird phylogenies. You shouldn't need to do that for any application, even a meta-analysis.
2. Try running it again. Server errors et al. are normally something to do with your Internet connection - just try one more time. DTD warnings can be safely ignored.
3. You'll get a Newick or a Nexus file out depending on the options you pick. Either can be loaded into R no problem - read.tree or read.nexus.

Let me know if this doesn't work for you - I might not get back to you until the weekend if there's very strange going on, but I will try!!!

Thanks again,

Will