Thanks to everyone for your quick responses!!

Responses to Draw Multiple Gene Trees:

Lars Arvestad's PrIMETV draws embedded trees: http://prime.sbc.su.se/

The authors provide a web-based version as well, which is very easy to use.
I was able to draw the individual gene trees within the same species tree,
then merge all the images in Adobe Illustrator.

DensiTree  http://www.cs.auckland.ac.nz/~remco/DensiTree/DensiTree.html

I used this program to illustrate the trees (>8000) produced by a Bayesian
run. Very effective for showing the major patterns plus their relative
occurrences.

Other Suggestions I did not try:

Dendroscope

http://topiaryexplorer.sourceforge.net/

Check out ms by R. R. Hudson:

http://home.uchicago.edu/~rhudson1/source/mksamples.html

Jaime Elizabeth Blair, PhD
Assistant Professor of Biology
Franklin & Marshall College
Lancaster PA 17604
Office (717) 291-3959
jaime.blair@fandm.edu
http://edisk.fandm.edu/jaime.blair

Jaime Blair <jaime.blair@fandm.edu>