# PAML Lab files for downlaod

2018 Workshop on Molecualr Evolution at the MBL

Follow this link to go to PAML Lab Activities page.

Follow this link to go to back to workshop wiki page.

## Download a full archive

You can download the necessary files from an archive here and then copy the files to your home directory on the cluster to do the excercises at the workshop.

Alternatively, you can use *wget* to download an archive to your home directoy on the cluster as follows:

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

If you just want to grab an individual file, use the links below.

## Files to download for exercise 1

The objective of this activity is to use CODEML to evaluate the likelihood of the GstD1 sequences for a variety of ω values. Plot log-likelihood scores against the values of ω and determine the maximum likelihood estimate of ω. Check your finding by running CODEML’s hill-climbing algorithm.

Step by step guide

ex1_codeml.ctl.txt

seqfile.txt

HelpFile.pdf

FigE1.pdf

## Files to download for exercise 2

In this exercise you will investigate the sensitivity of your estimate of ω to the transition/transversion ratio (κ), and to the assumed model for codon frequencies (πi’s). After you collect the required data you will determine which assumptions yield the largest and smallest values of S, and what effect it as on the value of ω.

Step by step guide

ex2_codml.ctl.txt

ex2_seqfile.txt

HelpFile.pdf

TableE2.pdf

## Files to download for exercise 3

The objective of this exercise is to use three LRTs to evaluate the following hypotheses: (1) the mutation rate of Ldh-C has increased relative to Ldh-A, (2) a burst of positive selection for functional divergence occurred following the duplication event that gave rise to Ldh-C, and (3) there was a long term shift in selective constraints following the duplication event that gave rise to Ldh-C.

Step by step guide

ex3_codeml.ctl

seqfile.txt

treeH0.txt

treeH1.txt

treeH2.txt

treeH3.txt

ex3_HelpFile.pdf

LDH_gene-tree.pdf

TableE3.pdf

## Files to download for exercise 4

The objective of this exercise is to use a series of LRTs to test for sites evolving under positive selection in the nef gene. If you find significant evidence for positive selection, then identify the involved sites by using empirical Bayes methods.

Step by step guide

ex4_codeml.ctl.txt

paml hiv2nef seqfile.txt

treeM0.txt

treeM1.txt

treeM2.txt

treeM3.txt

treeM7.txt

treeM8.txt

main HelpFile.pdf

rst HelpFile.pdf

TableE4.pdf