Tree Drawing

Doug.Eernisse at UB.CC.UMICH.EDU Doug.Eernisse at UB.CC.UMICH.EDU
Sun Sep 15 21:15:38 EST 1991


Dan Jacobson writes:
>Does anybody know of software which will plot phylogenic trees given 
>the standa rd nested parenthesis tree data?  I'm generating the tree 
>with the protpars program from PHYLIP and plotting it with drawtree 
>from PHYLIP however drawtree tends to print the name of one species 
>on top of the other if the branch tips are close together.  It is an 
>unrooted tree.
 
Other responses have emphasized DOS and Unix solutions. If you 
happen to have Macs available, there is another approach, although
it involves the commercial ($50) program PAUP, which draws great
trees in PICT format. Phylip is available, at least in version
3.3 on the Mac (anyone have version 3.4?), as is DRAWTREE.
 
If you are reluctant to use PAUP because this would require that
you change your data matrix format, you could use my freeware
HyperCard 2.x stack, DNA Translator, to do the conversion for you.
Among many other conversions, it will read in a PHYLIP.RESULT
 (output) text file, and convert it into a NEXUS format (PAUP,
MacClade in current 3.0+ versions). You would need to add a tree
block manually as follows:
 
begin trees;
	utree *mytree1 = ((((1,4),3),2),5);
	utree mytree2 = (((1,3),(2,4)),5);
end;
 
That is, add such a tree block to the end of the output NEXUS format
text file. Then execute the file in PAUP, the trees will be read
in automatically, and select "Print Trees" from the "Trees" menu.
Next, configure the tree format (font, margins, rectangular or
diagonal trees, etc.) to your desires and click on "Preview". 
You will see a screen version of the tree and be allowed to save
the tree as a PICT image. Anyone familiar with a Mac knows what
to do next (i.e., MacDraw, etc.), if you need further modifications,
however, PAUP will produce the printout just fine as well.
 
My stack, DNA Translator, is up to version .99.7, although this most
recent version is only available via anonymous ftp to my own account:
Ftp to ub.cc.umich.edu  --  login as 'anonymous' with any password,
Change directory 'cd gdef' and 'get dnastack'. You will need to
debinhex the resulting self-extracting archive (about 500K). The
stack also does some more flexible Protpars matrices (i.e., for
standard or vertebrate mtDNA codes) similar to PAUP. I have a
new XFCN that will generate a 'Protpars' matrix for any genetic
code, but haven't figured out how to do the tricky cases such as
Serine and stop codons, that require splitting up (sorry for this
complicated aside). The reason the stack is so large is that it
does many other things such as converting GenBank/EMBL formatted
sequence files into graphical, clickable, smart gene maps.
 
Doug Eernisse
Museum of Zoology
Univ. of Michigan
 
Doug_Eernisse at ub.cc.umich.edu or usergdef at umichub.bitnet




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