# Difference between revisions of "PAML notes"

PAML demo website: http://myweb.dal.ca/js551958/PAML_lab/lab.html

The details of the PAML demo can be found at the above website. Go to the above website first.

## For the lab

```   module load bioware
```
```   wget https://molevol.mbl.edu/images/d/df/PamlLab.zip
```
```   unzip PamlLab.zip
```
```   cd PamlLab
```

## Plotting for Exercise 1

Here are a couple examples of ways in which you might choose to plot your results.

Excel:

```   ColumnA --> Omegas
ColumnB --> lnL values
```
```   Select both
```
```   Navigate to: Insert --> Charts --> Scatter (choose lines)
```
```   Right click on X-axis (omegas) --> Format Axis --> Logarithmic scale
```

R

```    x_vector <- c(your parameter values, separated by commas)
```

For example: x_vector <- c(.005,.006,.007,.008)

```    y_vector <- c(your likelihoods, separated by commas)
plot(x = vector, y =y_vector, log="x", type="b")
```

## Codon Alignments

This is not part of the exercises, but you will need this information for running these kinds of analyses on your own datasets.

To fit codon models, you need a codon alignment (i.e. a nucleotide alignment that, when translated, corresponds perfectly to a good amino acid alignment). You can't just align nucleotides because most alignment programs don't look for codons, so the program may put gap characters in the middle of codons, throwing the sequences out of frame. You have to align the amino acids, and then force your unaligned nucleotides to fit that alignment.

We have shown you how to translate the nucleotides in SeaView and align amino acids using MAFFT or Muscle, but not how to get back to codons. The Pal2Nal server is good for this. You will upload your protein alignment and nucleotide sequences, and it will spit out the codon alignment. Please be aware that your raw nucleotides must be multiples of three (i.e. a full open reading frame) and free of stop codons.