# 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;

### Understanding the data file

The NEXUS file you just created has four blocks. The first block is a paup block that sets the `storebrlens` flag. This tells PAUP* to save branch lengths found in any trees. By default, PAUP* throws away branch lengths that it finds and estimates them. In this case, we are trying to get PAUP* to compute likelihoods for a tree in which all five branch lengths are set to the specific value 0.1, so it is important to get PAUP* to not discard branch lengths.

The second block is the data block. Data for two sites are provided, the first site being the one you used for homework #4. The second site is necessary because PAUP* will refuse to calculate the likelihood of a tree with data from only one site. We will simply ignore results for the second (dummy) site.

The third block is a trees block that defines the tree and branch lengths.

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*Can you find where in the tree description the length of the central branch is defined?*

The keyword `utree` can be used in PAUP* (but not necessarily other programs) to explicitly define an *unrooted* tree. The `hw4` part is just an arbitrary name for this tree: you could use any name here.

The fourth (paup) block comprises an `lset` command that specifies the likelihood settings. The `nst` option specifies the number of substitution parameters, which is 1 for the JC model, and `basefreq=equal` specifies that base frequencies are assumed to be equal. Together, `nst=1` and `basefreq=equal` specify the JC model because the only other model with one substitution parameter is the F81 model (which has unequal base frequencies).

The command `lscores 1` tells PAUP* to compute likelihood scores for the first tree in memory (which is the one we entered in this file). The keyword `userbrlen` tells PAUP* to use the branch lengths in the tree description (i.e. don't estimate branch lengths), and the `sitelike` keyword tells PAUP* to output the individual site likelihoods (the default behavior is to just output the overall likelihood).

Ok, go ahead and execute the file in PAUP* and see if your hand calculation in homework #4 was correct.