Workshop on Molecualr Evolution at the MBL
The links in ssection below allow you to download an individual file for a specific excercise.
Follow this link to go to back to PAML lab.
Follow this link to go to back to workshop schedule page.
Follow this link to go to back to the Bielawski faculty page.
Note that you can download all the necessary files at one time from an archive here.
[NOTE: I am updating and moving the archive; the download for the archive might be temporarily disabled.]
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.
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.
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.
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.