about Annotations file format and Tip Coloring by attribute

[Alonso]

Hi all,

I would like to know about two issues:

1)
Which is the right format for the Annotations File?
1.a) Is this file is just for loading the names of the annotations or
1.b) can I include attributes values for the tips in my tree.

Let's say:
1.a) Annotations File
attrib1
attrib2
attrib3
attrib4

1.b) Annotations File
Tip1 [attrib=0]
Tip2 [attrib=3]
Tip3 [attrib=9]
Tip4 [attrib=1]
Tip5 [attrib=6]

Is any of these a valid option? What is the right format?

2) If not in the Annotations file, is it possible to load a file with
attributes values for the tips (as in 1.b)

Thanks to all

Manuel

[Andrew Rambaut]

The annotations file is a simple tab-delimited file. The first row should have the
annotation names and the first column the taxon names. So:

taxa attrib1 attrib2
Tip1 1.0 1.0
Tip2 2.0 2.0
.
.

Andrew

___________________________________________________________________
Andrew Rambaut
Institute of Evolutionary Biology University of Edinburgh
Ashworth Laboratories Edinburgh EH9 3JT
EMAIL - a.ra...@ed.ac.uk TEL - +44 131 6508624

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[Alonso]

Hi Andrew,

Thanks a lot for your response.
I think I have correctly created and loaded the annotation file,
however I can not manage to have
colors in the tips based on the value of their attribute.

These are the steps I'm following

1- load the tree
2- import the annotations file. Tab-delimited with one Tip and
Attribute-value per line.
3- after importing the annotations I can see my attribute's label in
"Tip Labels - > Colour by"
4- I go to "Tip Labels - > Colour by" and choose my attribute but I
get no colors in the tree.
5- the only way of having colors in the tips is by defining the
attribute value tip by tip.
6- In the annotations file I changed the first column of the header
line from "taxa" to "clade" but without any better results.

If you have any clue about how to obtain a tree with tips colored
based on their attributes values I will appreciate that you let me
know.

Thanks a lot to you in advance.

Best,

manuel

PS:
- If you want I could send you the files with which I'm trying to
create my colored tree
- I'm using FigTree v1.3.1 on Ubuntu 9.04

>   EMAIL - a.ramb...@ed.ac.uk                TEL - +44 131 6508624