Question: Drawing phylogenetic tree in line format and Newick format from branch lengths
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gravatar for listerr01
3.8 years ago by
listerr010
United States
listerr010 wrote:

I used the Neighbor-joining algorithm on a distance matrix and obtained all the branch lengths - internal and external.  I need to now draw the tree - in both line format ("rectangular" format) and Newick format.  This seems silly, but I'm stuck with not knowing where or how to begin.

Note that I am not looking for any computer code at this point.  I'm just stuck with not knowing how to start - for either format.  Would appreciate any help.

Thanks,

Joe

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by listerr010
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gravatar for arnstrm
3.8 years ago by
arnstrm1.7k
Ames, IA
arnstrm1.7k wrote:

If you're not familiar with CLI, try using GUI programs such as MEGA, it is available for all platforms. You can easily load the alignments and construct different type so phylogenetic trees (ML, NJ, UPGMA etc). You can save the results as nwk format as well as render tree with that program.

 

ADD COMMENTlink written 3.8 years ago by arnstrm1.7k
0
gravatar for listerr01
3.8 years ago by
listerr010
United States
listerr010 wrote:

Hi arnstrm, thanks for the response.  Actually, I am very familiar with MEGA and use it on a regular basis.  I am writing code for another application that requires that I make the trees myself using code, not a GUI.  The part I am stuck at is not the code but the procedure for going from having computed all the branch lengths to actually depicting the tree in the form of a line diagram and in Newick format.

I am requesting help with that.

Thanks.

ADD COMMENTlink written 3.8 years ago by listerr010
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