3) IQ-Tree

#IQ-Tree

#Download from: http://www.iqtree.org/ 

cd Downloads/iqtree-1.6.12-MacOSX

#Run example first to ensure download correctly (code adapted from: http://www.iqtree.org/doc/Quickstart) :
bin/iqtree -s example.phy

#Make sure samples are in the Downlaods/iqtree folder before running:

bin/iqtree -s Mafricanum_aligned.fa
bin/iqtree -s Mbovis_alignment.fa
bin/iqtree -s Mtb_alignment.fa

#This can take anywhere from 5 minutes to 55 hours depending on the algorithms being computed for branch construction