IQ-TREE 2016

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IQ-TREE is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, IQ-TREE had been continually expanded to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. 1

Installed version(s)

The following versions are installed and currently available...

... on environment hpc-env/8.3:

  • IQ-TREE/1.6.12-foss-2019b
  • IQ-TREE/2.1.3-foss-2019b
  • IQ-TREE/2.1.3-intel-2019b

Loading / Using IQ-TREE

To load the desired version of the module, use the module load command, e.g.

module load hpc-env/8.3
module load IQ-TREE

Always remember: this command is case sensitive!

To find out on how to use IQ-TREEyou can just type in iqtree2 to print out a help text to get you started:

$ iqtree2

IQ-TREE multicore version 2.1.3 COVID-edition for Linux 64-bit built Jun 18 2021
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Command-line examples (replace 'iqtree2 ...' by actual path to executable):

1. Infer maximum-likelihood tree from a sequence alignment (example.phy)
   with the best-fit model automatically selected by ModelFinder:
     iqtree2 -s example.phy

2. Perform ModelFinder without subsequent tree inference:
     iqtree2 -s example.phy -m MF
   (use '-m TEST' to resemble jModelTest/ProtTest)

3. Combine ModelFinder, tree search, ultrafast bootstrap and SH-aLRT test:
     iqtree2 -s example.phy --alrt 1000 -B 1000

4. Perform edge-linked proportional partition model (example.nex):
     iqtree2 -s example.phy -p example.nex
   (replace '-p' by '-Q' for edge-unlinked model)

5. Find best partition scheme by possibly merging partitions:
     iqtree2 -s example.phy -p example.nex -m MF+MERGE
   (use '-m TESTMERGEONLY' to resemble PartitionFinder)

6. Find best partition scheme followed by tree inference and bootstrap:
     iqtree2 -s example.phy -p example.nex -m MFP+MERGE -B 1000

7. Use 4 CPU cores to speed up computation: add '-T 4' option

8. Polymorphism-aware model with HKY nucleotide model and Gamma rate:
     iqtree2 -s -m HKY+P+G

9. PoMo mixture with virtual popsize 5 and weighted binomial sampling:
     iqtree2 -s -m "MIX{HKY+P{EMP},JC+P}+N5+WB"

To show all available options: run 'iqtree2 -h'

Have a look at the tutorial and manual for more information:

At the root directory of IQ-TREE, you can find some example data, which you can use to get yourself familiar with the program. As a demonstrative example, this is how you could proceed (with or without usage of MPI):

## load environment and IQ-TREE module:
ml hpc-env/8.3 IQ-TREE/2.1.3-foss-2019b
## create dest dir and  copy test file (the error message ):
mkdir $HOME/iqtree_test && cd $HOME/iqtree_test && cp $EBROOTIQMINTREE/* .
## use iqtree2 with 4 threads on the example file:
iqtree2 -nt 4 -s example.phy
## use iqtree2 MPI-parallelised with 4 threads on the example file:
iqtree2-mpi -nt 4 -s example.phy

## look at the created output
ls -la


The full documentation can be found here.