Maximum Likelihood (Part 3: computer lab)

Instructions: Run and compare the results of both ML software (RAxML and IQ-Tree) on the toy dataset of primates. You can use my reproducible script as guideline: notebook-log.md.

• RAxML-NG
  • RAxML-NG tutorial 1 (HAL 1.3)
  • RAxML-NG tutorial 2 (newer)
• IQ-Tree

You can use the primates fasta file that you aligned with ClustalW, MUSCLE or T-Coffee, or you can use the toy data provided in the software tutorial.

Bonus points for paying attention to the importants aspects that affect the performance of the chosen method.

Double bonus points for comparing not only the performance of RAxML and IQ-Tree on a given alignment, but comparing how do results differ if we use an alignment from a different method. That is, primatesAA-aligned-muscle.fasta are the aligned sequences with MUSCLE. I can run RAxML and IQ-Tree on this file and compare the two trees. I can also run RAxML and IQ-Tree on primatesAA-aligned.fasta which was aligned with ClustalW and compare the 4 trees.

Homework

See the details of the Maximum Likelihood HW in here.