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I want to find the conventional phylogenetic tree of human, mouse, C elegans and drosophila, without all the other organisms. Do you know where can I get it?

thanks, Noga

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Are you looking to make one, or find one that someone else already made? I have a feeling that you wouldn't find one pre-made and that at best you'd have to do some deleting. You might also expand on what your end goal is, as I have a feeling a graph-kernel diagram might actually show what you want better. – Atl LED Feb 20 '14 at 15:45
I made some trees based on few enzymes and i want to compare them to the conventional tree. – user5790 Feb 20 '14 at 15:51
If you just want to check something, use the whole tree, you have all the information there. Just ignore the species you don't care about. – terdon Feb 20 '14 at 16:50
Every tree is an hypothesis of relationships. – kmm Feb 20 '14 at 18:07

This isn't a complete answer, but to get things rolling.

I think I see what you want; a comprehensive "correct" tree you can compare your single alignment tree to?

I can think of a couple of responses to this. Firstly there is no perfect way to make a phylogenetic tree. Aside from all the different distance metrics you could use and algorithms to sort large trees, the data you use can also vary depending on what you want to do. You can compare some conserved genes for long distance comparisons or highly mutable sequences for close distances, but which are subject to noise.

That being said a tree comparing ribosomal RNA is a phylogenetic standard. As are trees derived from multiple genes. If you want to see if your genes are unusual you can run a few other genes through the same comparison and see if the trees vary substantially for your gene. Because the animals you compare are so far apart on the tree the relative comparison will be pretty close to the tree you've made.

If you are trying to compare the tree quantitatively to some master tree, that will be a demanding task.

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You can go to Wikispecies and find the species page for each organism, e.g. the Mouse page. On there you can click on the Taxonavigation box Expand button and see the group names for the organism. Comparing the names for each organism will give the closest common ones, which gives you the tree.

However, for the tree between the mammals and the other two, you might want to have a look at the Tree of Life Web page for Bilateria. Your three groups fall into Deuterostomia, Arthropoda, and Nematoda; for these you'll find a tree for these three groups. (Actually two trees, but for your groups they amount to the same thing.)

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I would not recommend Wikispecies as a reference for phylogeny: taxonomic system is not identical to (our current understanding of) phylogenetic relationships. I'd not recommend Wikispecies at all, since it is currently occupied by a single moderator. – har-wradim Feb 21 '14 at 19:04

If you accept the nowadays prevailing Ecdysozoa-hypothesis the relationships are as follows:

               ____ Drosophila
       |      |____ C. elegans
  -----|       ____ Human
       |      |
              |____ Mouse

According to the more traditional views (the Coelomata-hypothesis):

         _______________ C. elegans
    ----|     __________ Drosophila
        |    |
        |____|       ____ Human
             |      |
                    |____ Mouse

(Note that these trees have the same unrooted topologies)

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