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iqtree

Basic tree search

# find the ML tree
iqtree -s example.aln -m LG -nt 4

# find the ML tree, using +G4 to model rate heterogeneity across sites
# using 4 discreet rate classes
iqtree -s example.aln -m LG+G4 -nt 4

# find the ML tree, using +F to take amino acid frequencies from the alignment
iqtree -s example.aln -m LG+G4+F -nt 4

# find the ML tree, using +C60 (or another mixture model) to model site classes
iqtree -s example.aln -m LG+C60+G4+F -nt 4

# find the ML tree, with non-parametric bootstraps
iqtree -s example.aln -m LG+G4 -nt 4 -b 100

# find the ML tree, with ultra-fast bootstraps
iqtree -s example.aln -m LG+G4 -nt 4 -bb 1000

Continuing a tree search

IQTREE has built-in checkpointing, meaning that if a tree search has crashed, you can continue from the last checkpoint Rerunning it with the same command line and input data will automatically resume the analysis from the last stopped point

The checkpoint information is writtin in .ckp.gz files. If you delete these files, your checkpointing information is lost!

# continue your tree search
iqtree -s example.aln -m LG -nt 4

# ignore checkpoints and redo the whole analysis from scratch
iqtree -s example.aln -m LG -nt 4 -redo

Add ultra-fast bootstraps to an already estimated ML tree

Estimate the likelihood of a tree given all parameters set

# -a sets the alpha shape parameter for gamma distribution
# -te constrains the tree search to the topology defined in the provided newick file
# -blfix constrains the branch lengths to those defined in the newick file
iqtree -s example.aln -m LG+G -a 0.5 -te constraint.newick -blfix

Tree search using Post Median Site Frequency (PMSF) mixture model



Topology Test




Tree search using Functional Divergence (FunDi) model


# taxon1,taxon2,taxon3 is all the taxa on one side of the fundi branch
# the other set is all taxa on the other side of the fundi branch and is inferred
# ,estimate tells iqtree to estimate Rho
iqtree -s example.aln -m LG+C60+F+G4 -te constraint.newick --fundi taxon1,taxon2,taxon3,estimate

# 0.60 tells iqtree to use a Rho of 0.60
iqtree -s example.aln -m LG+C60+F+G4 -te constraint.newick --fundi taxon1,taxon2,taxon3,0.60