species tree in Helmcop

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yizi yang

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Jun 2, 2012, 10:20:31 AM6/2/12
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Hi, everyone

I would like to get a species tree including species in Helmcop search
(parasitic nematodes+free living nematodes+platyhelminthes+host/
outgroups) with topology only according to their taxonomies, but I do
not know how to get such tree in newick format. Could anyone offer me
any suggestion?

Thanks a lot!

Yizi

John Martin

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Jun 5, 2012, 6:51:48 PM6/5/12
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One way to do that is to use the iTOL website (http://
itol.embl.de/). They have a tool that will dump newick format trees
from a list of species that you enter. Goto the page:

http://itol.embl.de/other_trees.shtml

and in the text field labeled "ID selection", enter all the HelmCoP
species in this format:

Brugia_malayi
Caenorhabditis_elegans
Caenorhabditis_brenneria
etc...

After entering all the species you want in the tree, press "Generate
tree" and it will print out a newick format version of your tree.
You can then copy-paste that tree into the "Data Upload" section
(http://itol.embl.de/upload.cgi) and it will draw a tree for you.
You will need to play around to get the exact appearance you want for
your tree. The basic output it gives you uses taxa ids I think, so
if you want the tree to display Latin species names you would have to
modify the newick format tree yourself. There are also other methods
in iTOL to decorate your tree with colors and so forth. You will
need to read the documentation on that site to learn all the tricks to
make a good looking tree.



John

Ionit

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Jun 29, 2012, 3:43:28 AM6/29/12
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Hi,

I recently worked on the iTOL like John Martin told you. It is indeed a fantastic tool.
I highly recomend you to read the tutorial to take even better advantage of all the option present in this tool!

Sincerely:
Ionit
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