PAML Lab resources

2018 Workshop on Molecualr Evolution at the MBL

Follow this link to go to back to PAML Lab Activities page.

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

Useful documents

You can download the necessary files from an archive

You can download individual files here.

The PAML lab slides: PamlDemo.pdf.

Here is a copy of the book chapter that accompanies the lab exercises: Book_Chapter.pdf.

Here is a copy of the PAML user manual: pamlDOC.pdf.

Here is a copy of the PAML FAQ user manual: pamlFAQs.pdf.

Here is a copy of the paper for PAML4: Yang2007MBE.

A book chapter inlcuding a discussion of workflow, experimental design and best practices: UNIT6.15.pdf.

An example of a 2-phase approach to "best practices" focused on quality control and robustness: BakerGenetics2016.

A comprehensive review of the major inference challeneges under codon models: Jones InPress.

Lecture slides part 1 and part 2: [link]

Lecture sleides part 3: [link]

Useful links

Very helpful Chi-Square calculator on-line: Chi-Square Calculator

My home page (shamefully out of date):

Ziheng Yang's page:

PAML page:

HyPhy page: http//

DataMonkey Adaptive Evolution Server:

COLD program documentation and download:

The PAML Dicussion Group (Google group):!forum/pamlsoftware.