Pretty phylogenetic dendrogram from jalview

Jalview Discussion
#1

Hi ,
I wanted to make a dendrogram (like the one here:
http://en.wikipedia.org/wiki/Phylogenetic_tree ). For an alignment and
tree calculated inside Jalview/clustalw
I am interested in something that creates a publication manipulatable
format like Adobe Illustrator or EPS.

Does anyone have any ideas . Also I am curious how to get the tree
output from Jalview into that recommended program.

Thanks in advance
Hari

#2

Hi Hari,

In the window where the tree is drawn in Jalview, go to File > output to textbox. This will give you the tree in Newick format. >From just a google search of “phylogenetic tree drawers” I found this:

http://iubio.bio.indiana.edu/treeapp/treeprint-form.html
http://www.phylodiversity.net/rree/drawtree/index.html

You can input the Newick format and the programs will draw the tree for you.

Here is also a very long list of tree editors:

http://bioinfo.unice.fr/biodiv/Tree_editors.html

Hope that helps!

Lauren

···

On Thu, May 13, 2010 at 12:02 PM, hari jayaram <harijay@gmail.com> wrote:

Hi ,
I wanted to make a dendrogram (like the one here:
http://en.wikipedia.org/wiki/Phylogenetic_tree ). For an alignment and
tree calculated inside Jalview/clustalw
I am interested in something that creates a publication manipulatable
format like Adobe Illustrator or EPS.

Does anyone have any ideas . Also I am curious how to get the tree
output from Jalview into that recommended program.

Thanks in advance
Hari

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#3

Thanks to Reza Khayat and Lauren Hui,

Here is a summary of the responses to my question:
Reza suggested SplitsTree (www.splitstree.org). There's also
Optimage (http://www.manchester.ac.uk/bioinformatics/optimage/) that
allows you to do the tree in 3D.

Laurens email is reproduced below.

Thanks a tonne everyone.
Hari

In the window where the tree is drawn in Jalview, go to File > output
to textbox. This will give you the tree in Newick format. From just a
google search of "phylogenetic tree drawers" I found this:

http://iubio.bio.indiana.edu/treeapp/treeprint-form.html
http://www.phylodiversity.net/rree/drawtree/index.html

You can input the Newick format and the programs will draw the tree for you.

Here is also a very long list of tree editors:

http://bioinfo.unice.fr/biodiv/Tree_editors.html

Hope that helps!

Lauren

···

On Thu, May 13, 2010 at 3:02 PM, hari jayaram <harijay@gmail.com> wrote:

Hi ,
I wanted to make a dendrogram (like the one here:
http://en.wikipedia.org/wiki/Phylogenetic_tree ). For an alignment and
tree calculated inside Jalview/clustalw
I am interested in something that creates a publication manipulatable
format like Adobe Illustrator or EPS.

Does anyone have any ideas . Also I am curious how to get the tree
output from Jalview into that recommended program.

Thanks in advance
Hari