Question: How to read the numbers at the end of a leaf node for my phylogenetic tree?
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gravatar for atwalmanpreet
2.1 years ago by
atwalmanpreet0 wrote:

Hi,

I've been searching for hours now for an answer to my question but have had no luck and am getting increasingly confused.

So I have created a phylogenetic tree, but I do not understand the meaning of the numbers on my leaf nodes i.e. at the end of the branches. Could someone please describe the meaning of these numbers to me? I've posted an example below.

http://postimg.org/image/fzk2tvg0n/

This link is not a virus, it just redirects you to look at the image!

Many thanks in advance.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by atwalmanpreet0
1

There's no link to the tree. Anyway, the numbers can be anything you or your software decided to put there so without information on what you did, there's little chance anyone can tell you what these numbers are.

ADD REPLYlink written 2.1 years ago by Jean-Karim Heriche18k

Hi,

Thank you for your reply. I've updated the link, so you should be able to see the numbers I was mentioning.

I used a programme called MUSCLE to create a neighbour- joining phylogenetic tree of NMDA subunits between humans and zebrafish. The software automatically puts these numbers at the end.

ADD REPLYlink written 2.1 years ago by atwalmanpreet0

As @Jean-Karim said the tip labels can be pretty much anything. I have only used MUSCLE for doing the alignments, not to create a neighbour-joining tree.We really need to see the tree to have an idea of what may be going on. What program are you using to view the tree? Are the branches labelled with branch lengths?

ADD REPLYlink written 2.1 years ago by Dan Gaston7.1k

https://postimg.org/image/b814tlmyv/

This is the link to the whole tree, I'm just viewing the phylogenetic tree directly from the MUSCLE webpage and as you can see from the link the branches are not labelled.

ADD REPLYlink written 2.1 years ago by atwalmanpreet0

Still not sure exactly what website you are viewing this on. I don't think the core MUSCLE website has a web interface to the program or an interface to viewing a tree file. My guess is that for whatever reason the program displaying the tree is displaying the terminal branch lengths after the node name. You can download the actual tree data and open it in a text file to confirm.

ADD REPLYlink written 2.1 years ago by Dan Gaston7.1k
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