Phylogenetics: Likelihood Lab
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EEB 349: Phylogenetics | |
The goal of this lab exercise is to show you how to conduct maximum likelihood analyses in PAUP* using several models |
Contents
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;