[Taxacom] RES: phylogenetic software for undergrad class

[Vitor Fernandes O. de Miranda]

Hi Lena,

 

For my classes on phylogeny (including lab classes) I strongly recommend:

 

* BioEdit

- For DNA and protein alignments (based on Clustal)

-  For checking and manual (“eye”) edition of matrices

 

* Paup/ PaupUp/ TNT

- For parsimony, ML and cluster analyses (molecular and morpho matrices)

Using Windows interface is not so attractive (the menu-based is possible
only in Mac version), so you can use PaupUp to have a user friendly
interface (with menus).

As Paup is not for free, TNT is a good option (it’s free). With TNT it’s
also possible to create numeric (morpho, etc.) matrices.

 

* TreeView and FigTree

Both free and good options to tree drawing.

 

That’s my two cents.

 

Best wishes,

Vitor.

 

BioEdit

 <http://www.mbio.ncsu.edu/bioedit/bioedit.html>
http://www.mbio.ncsu.edu/bioedit/bioedit.html

 

Paup

 <http://paup.csit.fsu.edu/> http://paup.csit.fsu.edu/

 

PaupUp

 <http://www.agro-montpellier.fr/sppe/Recherche/JFM/PaupUp/main.htm>
http://www.agro-montpellier.fr/sppe/Recherche/JFM/PaupUp/main.htm

 

TNT

 <http://www.zmuc.dk/public/phylogeny/tnt/>
http://www.zmuc.dk/public/phylogeny/tnt/

 

FigTree

 <http://tree.bio.ed.ac.uk/software/figtree/>
http://tree.bio.ed.ac.uk/software/figtree/

 

TreeView

 <http://taxonomy.zoology.gla.ac.uk/rod/treeview.html>
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html 

_______________________________

Prof.Dr. Vítor Fernandes Oliveira de Miranda 

Universidade Estadual Paulista – UNESP
Campus Jaboticabal
Departamento de Biologia Aplicada à Agropecuária
Faculdade de Ciências Agrárias e Veterinárias – FCAV
Via de Acesso Prof. Paulo Donato Castellane s/n
CEP 14884-900     Jaboticabal – SP – Brasil

Fone: +55 (16) 3209-2620  Ramal 213

email:  <mailto:vmiranda at fcav.unesp.br> vmiranda at fcav.unesp.br   Skype:
vmirandum

 

De: taxacom-bounces at mailman.nhm.ku.edu
[mailto:taxacom-bounces at mailman.nhm.ku.edu] Em nome de Lena Struwe
Enviada em: terça-feira, 12 de abril de 2011 13:26
Para: Taxacom
Assunto: [Taxacom] phylogenetic software for undergrad class

 

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

--
*************************************
Dr. Lena Struwe
Associate Professor
Dept. of Ecology, Evolution,&  Natural Resources/ Dept. of Plant Biology&
Pathology
Rutgers University
237 Foran Hall, 59 Dudley Road
New Brunswick, NJ 08901-8551, USA
phone: (732) 932-9711 ext. 235, fax: (732) 932-9441
e-mail: struwe at aesop.rutgers.edu
home page: www.rci.rutgers.edu/~struwe
GENTIAN RESEARCH NETWORK: http://gentian.rutgers.edu
Director, CHRYSLER HERBARIUM: http://herbarium.rutgers.edu





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