Phylogenetics: Likelihood Lab

From EEBedia
Revision as of 02:23, 7 February 2007 by PaulLewis (Talk | contribs)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search
Template:Under Construction
Adiantum.png EEB 349: Phylogenetics
The goal of this lab exercise is to show you how to conduct maximum likelihood analyses in PAUP* using several models

Part A: Using PAUP* to check your answers for homework #4

Create a data file

Create a new file in PAUP* and enter the following text:


begin paup;
  set storebrlens;

begin data;
  dimensions ntax=4 nchar=2;
  format datatype=dna;
    taxon1 AA
    taxon2 AC
    taxon3 CG
    taxon4 TT

begin trees;
  utree hw4 = (taxon1:0.1, taxon2:0.1, (taxon3:0.1, taxon4:0.1):0.1);

begin paup;
  lset nst=1 basefreq=equal;
  lscores 1 / userbrlen sitelike;

Understanding the data file

Part B:

References cited