Re: Annotations in Fig tree

[Baika Levi]

Hi Adrian
I have similar questions. If you have figured out this can you please share your method? An R script would also work if you have it.

Thanks

Levi

On Tuesday, April 23, 2013 7:13:19 AM UTC-4, adrien...@gmail.com wrote:

Hello there,

I have two questions regarding the use of Figtree:

1) I'm experiencing issues trying to import and use annotations file in Fig tree to generate annotated and colored trees.

I read all I could find on the google group but still...I assume there is some formatting errors in m file. Or is there any known related bug ?

Reading that " The annotations file is a simple tab-delimited file in which the first row should have the annotation names and the first column the taxon names", I'd like to know if the annotations value can be qualitative ? (location for instance) or if it has to be coded with number ? Is there any special formatting ? (" or ' or any other signs)...
I have attached my tree and annotations file. I'm using Figtree 1.4.0 on windows and it crush. I've tried different modifications without any success....

Thanks to be in touch if someone has a solution. I'm currently trying to use R to generate nice trees but I would rather keep on using Figtree if possible.
Would it be possible to get any well-working example annotation file ?

2) Is there a way to differentiate between the tips and the nodes ? I mean, I'd be keen to generate a tree without tips ID but including symbols (squares for instance) at tips and coloring those symbols according to location of the strains for instance. This apply for tips and not for nodes that's why I would like to apply different settings to tips and internal nodes.

Cheers
Adrien

[Simon Uribe-Convers]

Hey Adrien,

you probably already solved this, but I was having a similar problem with FigTree 1.4.0 and my annotations table. I solved it by using FigTree 1.3.1, so I'm assuming it's a bug on 1.4.0.

I've attached my annotation table in case you want to look at it.

2) Is there a way to differentiate between the tips and the nodes ?

No idea but it would be cool.

Cheers,
Simon

[Simon Uribe-Convers]

Wrong annotation file!! oops!

Here is the one that actually works! Sorry for the confusion.