Phylogenetics: Using IQ-TREE for multilocus likelihood analyses
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EEB 5349: Phylogenetics |
Goals
Today you will continue learning about maximum likelihood inference and will learn to use a program known for its speed and ability to handle large-scale phylogenetic analyses. IQ-TREE is not the only software that does this: you may later wish to visit the Phylogenetics: Large Scale Maximum Likelihood Analyses lab and note that there is also an alternative IQ-Tree written by Kevin Keegan for the 2018 version of EEB-5349.
Getting started
Login to your account on the Health Center (Xanadu) cluster (ssh username@xanadu-submit-ext.cam.uchc.edu). Type the following:
srun --qos=general --pty bash
to start a session on a node that is not currently running jobs. Once you see the prompt, type
module load paup/4.0a-166
to load the paup module.
Which rate heterogeneity submodels provide the largest boost to the likelihood?
Why do pinvar and shape change the way they do when estimated jointly versus separately?
