[Taxacom] phylogenetic software for undergrad class

[Timothy Jones]

 Geneious for the DNA and Mesquite for the morph.
Geneious costs real money but is available fully functional for a two week
trial I believe, so time it accordingly and you can save your money.
http://www.geneious.com/default,28,downloads.sm
It has multiple choices for aligning seqs including MAFFT which takes
seconds/minutes to run even on large datasets of hundreds to a couple of
 thousand.     Tree building with PHYML,  Bayes, and PAUP (you need a copy
of PAUP and the path to it)  easily run through installing plugins (super
easy)  plus uses a  graphical interface, no command line stuff here.
Mesquite is free (bonus!) and building morph matrices is relatively
painless.  http://mesquiteproject.org/mesquite/download/download.html

Tim


On Tue, Apr 12, 2011 at 11:25 AM, Lena Struwe <struwe at aesop.rutgers.edu>wrote:

> Hi everybody -
>
> If you have to teach just one basic lab for students where they have to
> run a simple phylogenetic analysis of DNA+morphology and using parsimony
> and likelihood, what software would you recommend that is user-friendly,
> free, easy to learn, and so on? This is just for a lab, not a whole
> class, and to get students to at least get a first hands-on experience
> with running a simple analysis. I would like to use a program that is
> visually pleasing, can handle at least small datasets, and uses the
> Nexus format for import. Any suggestions and recommendations?
>
> best
>
> Lena Struwe
>
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-- 
Timothy M. Jones
Louisiana State University
Baton Rouge, LA 70803
Website - http://www.herbarium.lsu.edu/keys/