Difference between revisions of "Phylogenetics: Using IQ-TREE for multilocus likelihood analyses"

From EEBedia
Jump to: navigation, search
(Created page with "{| border="0" |- |rowspan="2" valign="top"|200px |<span style="font-size: x-large">[http://phylogeny.uconn.edu/courses/ EEB 5349: Phylogenetics]</span>...")
(No difference)

Revision as of 12:40, 10 February 2020

Adiantum.png EEB 5349: Phylogenetics


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?