Many thanks to everyone who replied to my earlier post seeking a windows alternative to MacClade for teaching systematics in intro bio labs. I received over 2 dozen replies within 24 hours. Several folks asked me to post a summary of the replies. Over 90% suggested Mesquite, which is a JAVA based program also written by the Maddisons (the authors of MacClade) Information on mesquite is available here http://mesquiteproject.org/mesquite/mesquite.html Steve Jordan at Bucknell (see 1st post below) has general instructions on Mesquite for his intro bio students that folks are welcome to check out. A selection of the replies I got is below: ----- I was faced with this same problem several years ago, and found Mesquite to be a good alternative. We've used Mesquite to teach systematics labs now to hundreds of students on PCs and Macs without any major problems. A nice aspect of Mesquite is the fact that it is platform-independent, so the instructions can be virtually identical for PC or Mac users. It is also freeware. Here is a link to our lab website. The labs that use Mesquite are numbers 3 and 4. Feel free to use or modify these if you'd like. http://www.departments.bucknell.edu/biology/courses/core/biol208/labs/ Thanks, Steve Steve Jordan, Associate Professor Department of Biology Bucknell University Lewisburg, PA 17837 Office: 302 Bio. Bldg. +1 570-577-1254 Lab: 331 Bio. Bldg. +1 570-577-3816 Fax: +1 570-577-3537 http://www.facstaff.bucknell.edu/sdjordan/jordan.html Have you tried PAUP (licensed) or PHYLIP (free)? Birgit I think there is a windows program called CLADOS that does the same thing as MacClade does. I have not used in a long time. was going to suggest mesquite which is free & available on windows. there is also used a web-based program, swami --http://www.ngbw.org/. hope you are doing well- I used to use WinClada. That still might work. Please let me know if you find something better. I am pretty sure the exercise could be done in R (which is free), just not confident about calculating CI values in R since I have not done it. There is an excellent resource also about how to do many phylogenetic analyses/manipulations in R located here: http://www.r-phylo.org/wiki/HowTo_Table_of_Contents Using R would also be a great way to introduce students to command line coding software, which is a really valuable skill. I would recommend MEGA for doing cursory alignments and tree constructions on a PC. http://www.megasoftware.net/ I'm not sure about swapping branches in MEGA but it may be easy to import a tree from MEGA into another tree viewing program such as FigTree. ----- Sarah Gilman, Ph.D. Joint Science Department Keck Science Center The Claremont Colleges 925 N. Mills Avenue Claremont, CA 91711 http://faculty.jsd.claremont.edu/sgilman sgilman@jsd.claremont.edu 909-607-0715 Sarah Gilman