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I'm trying to look at relationships between parasite and host phylogenetic trees. I have done a bit of searching for a software in which to do this with, and I have tried using Dendroscope and TreeMap, but can't get to grips with them.

I want to produce something along the lines of this;

enter image description here

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1  
Treemap and Dendroscope are the only ones that I know of. Can you start small? Search for examples like: ib.berkeley.edu/courses/ib200b/ib200b_2009/Labs/… and try to work through. –  kmm Apr 26 at 14:48
    
I think that I may have underestimated the complexity of the matter. That run through is very useful, however it is the very earliest stage that I am struggling with. I have two phylogenetic trees (one host and one parasite). Both are in newick format. In this manual it says "This file contains two trees, one for the host and one for the parasite, and a description of which hosts are associated with which parasites.". I think the lack of description of association is the problem. I assumed the software would take the associations from the information in the trees? I'm not an expert! –  Will Perry Apr 26 at 21:10

2 Answers 2

up vote 3 down vote accepted

Dendroscope

Using Dendroscope, I opened the provided example file trees.new. This opens a new window with 16 trees in it.

  1. Shift click on the first two trees (Tree1 and Tree2).
  2. Choose Algorithms $\rightarrow$ Tanglegram...
  3. This will compute the tanglegram and open a new window.

At this point, I get:

Tanglegram

There is nothing special in the trees.new file, just 16 Newick trees. So it looks like all you need is to have your trees in the same file or use File $\rightarrow$ Add from file.

I think that the tricky part is that your trees have to have the same tip labels, so that they can be lined up optimally. So in your example, Phalacrocorax pygmaeus and Pectinopygus excornis must have been named the same in the original Nexus file and then modified to produce the final figure.

TreeMap 3

TreeMap requires some preliminary setup. Basically you create a Nexus file manually. Using the 4taxonmatch file from the examples, you can get the basic layout. You have a HOST block and a PARASITE block. Within each one of those is a TREE block, which contains the Newick formatted tree.

The RANGE block inside the DISTRIBUTION block contains the mapping table. Here p maps to u, etc. This is the connection between host and parasite.

#NEXUS
BEGIN HOST; 
TREE * Host1 = (u, (v, (w, x))); 
ENDBLOCK; 

BEGIN PARASITE;
TREE * Para1 = (p, (q, (r, s))); 
ENDBLOCK; 

BEGIN DISTRIBUTION; 
RANGE 
    p: u, 
    q: v, 
    r: w, 
    s: x
; 
END;

In contrast, you get the correctly labelled tree directly. See below.

Tanglegram 2

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Brillian,it was the tip labels in Dendroscope. I understand how these work now, thank you! –  Will Perry Apr 27 at 17:22

I have to confess that I know nothing about phylogenetics and the associated softwares but according to the abstract of this article it seems that they used BEAST to map coalescence of co-evolving hosts and parasites.

Also this article is probably of highest interest to you as it compares the efficiency of different softwares to construct tanglegrams

Let me know if I missed your point so that I can delete this answer ;-)

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That makes two of us! I shall try and use dendoscope again with that article in mind. Thank you! –  Will Perry Apr 26 at 21:21

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