Phylogenetics: Likelihood Lab

Template:Under Construction

	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:

#nexus

begin paup;
  set storebrlens;
end; 

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

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

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