IQ-Tree-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.2.2.7, 2.3.5, 2.3.6, 3.0.1

Author / Distributor

Please see http://www.iqtree.org/

Description

Efficient phylogenomic software by maximum likelihood. More information: http://www.iqtree.org/

Running Program

• Version 2.3.6, installed in /apps/eb/IQ-TREE/2.3.6-gompi-2023a

To use this version of IQ-TREE, please first load the module with

module load IQ-TREE/2.3.6-gompi-2023a

• Version 3.0.1, installed in /apps/eb/IQ-TREE/3.0.1-gompi-2024a

To use this version of IQ-TREE, please first load the module with

module load IQ-TREE/3.0.1-gompi-2024a

Sample job submission script (sub.sh) to run IQ-Tree version 2.3.6:

#!/bin/bash
#SBATCH --job-name=jobName
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=2gb
#SBATCH --time=04:00:00
#SBATCH --output=IQTREE.%j.out
#SBATCH --error=IQTREE.%j.err

cd $SLURM_SUBMIT_DIR

module load IQ-TREE/2.3.6-gompi-2023a
iqtree2 [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

module load IQ-TREE/2.3.6-gompi-2023a

iqtree2 -h
IQ-TREE multicore version 2.3.6 for Linux x86 64-bit built May  5 2025
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt,
Dominik Schrempf, Michael Woodhams, Ly Trong Nhan, Thomas Wong

Usage: iqtree [-s ALIGNMENT] [-p PARTITION] [-m MODEL] [-t TREE] ...

GENERAL OPTIONS:
  -h, --help           Print (more) help usages
  -s FILE[,...,FILE]   PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s)
  -s DIR               Directory of alignment files
  --seqtype STRING     BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)
  -t FILE|PARS|RAND    Starting tree (default: 99 parsimony and BIONJ)
  -o TAX[,...,TAX]     Outgroup taxon (list) for writing .treefile
  --prefix STRING      Prefix for all output files (default: aln/partition)
  --seed NUM           Random seed number, normally used for debugging purpose
  --safe               Safe likelihood kernel to avoid numerical underflow
  --mem NUM[G|M|%]     Maximal RAM usage in GB | MB | %
  --runs NUM           Number of indepedent runs (default: 1)
  -v, --verbose        Verbose mode, printing more messages to screen
  -V, --version        Display version number
  --quiet              Quiet mode, suppress printing to screen (stdout)
  -fconst f1,...,fN    Add constant patterns into alignment (N=no. states)
  --epsilon NUM        Likelihood epsilon for parameter estimate (default 0.01)
  -T NUM|AUTO          No. cores/threads or AUTO-detect (default: 1)
  --threads-max NUM    Max number of threads for -T AUTO (default: all cores)

CHECKPOINT:
  --redo               Redo both ModelFinder and tree search
  --redo-tree          Restore ModelFinder and only redo tree search
  --undo               Revoke finished run, used when changing some options
  --cptime NUM         Minimum checkpoint interval (default: 60 sec and adapt)

PARTITION MODEL:
  -p FILE|DIR          NEXUS/RAxML partition file or directory with alignments
                       Edge-linked proportional partition model
  -q FILE|DIR          Like -p but edge-linked equal partition model 
  -Q FILE|DIR          Like -p but edge-unlinked partition model
  -S FILE|DIR          Like -p but separate tree inference
  --subsample NUM      Randomly sub-sample partitions (negative for complement)
  --subsample-seed NUM Random number seed for --subsample

LIKELIHOOD/QUARTET MAPPING:
  --lmap NUM           Number of quartets for likelihood mapping analysis
  --lmclust FILE       NEXUS file containing clusters for likelihood mapping
  --quartetlh          Print quartet log-likelihoods to .quartetlh file

TREE SEARCH ALGORITHM:
  --ninit NUM          Number of initial parsimony trees (default: 100)
  --ntop NUM           Number of top initial trees (default: 20)
  --nbest NUM          Number of best trees retained during search (defaut: 5)
  -n NUM               Fix number of iterations to stop (default: OFF)
  --nstop NUM          Number of unsuccessful iterations to stop (default: 100)
  --perturb NUM        Perturbation strength for randomized NNI (default: 0.5)
  --radius NUM         Radius for parsimony SPR search (default: 6)
  --allnni             Perform more thorough NNI search (default: OFF)
  -g FILE              (Multifurcating) topological constraint tree file
  --fast               Fast search to resemble FastTree
  --polytomy           Collapse near-zero branches into polytomy
  --tree-fix           Fix -t tree (no tree search performed)
  --treels             Write locally optimal trees into .treels file
  --show-lh            Compute tree likelihood without optimisation
  --terrace            Check if the tree lies on a phylogenetic terrace

ULTRAFAST BOOTSTRAP/JACKKNIFE:
  -B, --ufboot NUM     Replicates for ultrafast bootstrap (>=1000)
  -J, --ufjack NUM     Replicates for ultrafast jackknife (>=1000)
  --jack-prop NUM      Subsampling proportion for jackknife (default: 0.5)
  --sampling STRING    GENE|GENESITE resampling for partitions (default: SITE)
  --boot-trees         Write bootstrap trees to .ufboot file (default: none)
  --wbtl               Like --boot-trees but also writing branch lengths
  --nmax NUM           Maximum number of iterations (default: 1000)
  --nstep NUM          Iterations for UFBoot stopping rule (default: 100)
  --bcor NUM           Minimum correlation coefficient (default: 0.99)
  --beps NUM           RELL epsilon to break tie (default: 0.5)
  --bnni               Optimize UFBoot trees by NNI on bootstrap alignment

NON-PARAMETRIC BOOTSTRAP/JACKKNIFE:
  -b, --boot NUM       Replicates for bootstrap + ML tree + consensus tree
  -j, --jack NUM       Replicates for jackknife + ML tree + consensus tree
  --jack-prop NUM      Subsampling proportion for jackknife (default: 0.5)
  --bcon NUM           Replicates for bootstrap + consensus tree
  --bonly NUM          Replicates for bootstrap only
  --tbe                Transfer bootstrap expectation

SINGLE BRANCH TEST:
  --alrt NUM           Replicates for SH approximate likelihood ratio test
  --alrt 0             Parametric aLRT test (Anisimova and Gascuel 2006)
  --abayes             approximate Bayes test (Anisimova et al. 2011)
  --lbp NUM            Replicates for fast local bootstrap probabilities

MODEL-FINDER:
  -m TESTONLY          Standard model selection (like jModelTest, ProtTest)
  -m TEST              Standard model selection followed by tree inference
  -m MF                Extended model selection with FreeRate heterogeneity
  -m MFP               Extended model selection followed by tree inference
  -m ...+LM            Additionally test Lie Markov models
  -m ...+LMRY          Additionally test Lie Markov models with RY symmetry
  -m ...+LMWS          Additionally test Lie Markov models with WS symmetry
  -m ...+LMMK          Additionally test Lie Markov models with MK symmetry
  -m ...+LMSS          Additionally test strand-symmetric models
  --mset STRING        Restrict search to models supported by other programs
                       (raxml, phyml, mrbayes, beast1 or beast2)
  --mset STR,...       Comma-separated model list (e.g. -mset WAG,LG,JTT)
  --msub STRING        Amino-acid model source
                       (nuclear, mitochondrial, chloroplast or viral)
  --mfreq STR,...      List of state frequencies
  --mrate STR,...      List of rate heterogeneity among sites
                       (e.g. -mrate E,I,G,I+G,R is used for -m MF)
  --cmin NUM           Min categories for FreeRate model [+R] (default: 2)
  --cmax NUM           Max categories for FreeRate model [+R] (default: 10)
  --merit AIC|AICc|BIC  Akaike|Bayesian information criterion (default: BIC)
  --mtree              Perform full tree search for every model
  --madd STR,...       List of mixture models to consider
  --mdef FILE          Model definition NEXUS file (see Manual)
  --modelomatic        Find best codon/protein/DNA models (Whelan et al. 2015)

PARTITION-FINDER:
  --merge              Merge partitions to increase model fit
  --merge greedy|rcluster|rclusterf
                       Set merging algorithm (default: rclusterf)
  --merge-model 1|all  Use only 1 or all models for merging (default: 1)
  --merge-model STR,...
                       Comma-separated model list for merging
  --merge-rate 1|all   Use only 1 or all rate heterogeneity (default: 1)
  --merge-rate STR,...
                       Comma-separated rate list for merging
  --rcluster NUM       Percentage of partition pairs for rcluster algorithm
  --rclusterf NUM      Percentage of partition pairs for rclusterf algorithm
  --rcluster-max NUM   Max number of partition pairs (default: 10*partitions)

SUBSTITUTION MODEL:
  -m STRING            Model name string (e.g. GTR+F+I+G)
                 DNA:  HKY (default), JC, F81, K2P, K3P, K81uf, TN/TrN, TNef,
                       TIM, TIMef, TVM, TVMef, SYM, GTR, or 6-digit model
                       specification (e.g., 010010 = HKY)
             Protein:  LG (default), Poisson, cpREV, mtREV, Dayhoff, mtMAM,
                       JTT, WAG, mtART, mtZOA, VT, rtREV, DCMut, PMB, HIVb,
                       HIVw, JTTDCMut, FLU, Blosum62, GTR20, mtMet, mtVer, mtInv, FLAVI,
			Q.LG, Q.pfam, Q.pfam_gb, Q.bird, Q.mammal, Q.insect, Q.plant, Q.yeast
     Protein mixture:  C10,...,C60, EX2, EX3, EHO, UL2, UL3, EX_EHO, LG4M, LG4X
              Binary:  JC2 (default), GTR2
     Empirical codon:  KOSI07, SCHN05
   Mechanistic codon:  GY (default), MG, MGK, GY0K, GY1KTS, GY1KTV, GY2K,
                       MG1KTS, MG1KTV, MG2K
Semi-empirical codon:  XX_YY where XX is empirical and YY is mechanistic model
      Morphology/SNP:  MK (default), ORDERED, GTR
      Lie Markov DNA:  1.1, 2.2b, 3.3a, 3.3b, 3.3c, 3.4, 4.4a, 4.4b, 4.5a,
                       4.5b, 5.6a, 5.6b, 5.7a, 5.7b, 5.7c, 5.11a, 5.11b, 5.11c,
                       5.16, 6.6, 6.7a, 6.7b, 6.8a, 6.8b, 6.17a, 6.17b, 8.8,
                       8.10a, 8.10b, 8.16, 8.17, 8.18, 9.20a, 9.20b, 10.12,
                       10.34, 12.12 (optionally prefixed by RY, WS or MK)
      Non-reversible:  STRSYM (strand symmetric model, equiv. WS6.6),
                       NONREV, UNREST (unrestricted model, equiv. 12.12)
                       NQ.pfam, NQ.bird, NQ.mammal, NQ.insect, NQ.plant, NQ.yeast
           Otherwise:  Name of file containing user-model parameters

STATE FREQUENCY:
  -m ...+F             Empirically counted frequencies from alignment
  -m ...+FO            Optimized frequencies by maximum-likelihood
  -m ...+FQ            Equal frequencies
  -m ...+FRY           For DNA, freq(A+G)=1/2=freq(C+T)
  -m ...+FWS           For DNA, freq(A+T)=1/2=freq(C+G)
  -m ...+FMK           For DNA, freq(A+C)=1/2=freq(G+T)
  -m ...+Fabcd         4-digit constraint on ACGT frequency
                       (e.g. +F1221 means f_A=f_T, f_C=f_G)
  -m ...+FU            Amino-acid frequencies given protein matrix
  -m ...+F1x4          Equal NT frequencies over three codon positions
  -m ...+F3x4          Unequal NT frequencies over three codon positions

RATE HETEROGENEITY AMONG SITES:
  -m ...+I             A proportion of invariable sites
  -m ...+G[n]          Discrete Gamma model with n categories (default n=4)
  -m ...*G[n]          Discrete Gamma model with unlinked model parameters
  -m ...+I+G[n]        Invariable sites plus Gamma model with n categories
  -m ...+R[n]          FreeRate model with n categories (default n=4)
  -m ...*R[n]          FreeRate model with unlinked model parameters
  -m ...+I+R[n]        Invariable sites plus FreeRate model with n categories
  -m ...+Hn            Heterotachy model with n classes
  -m ...*Hn            Heterotachy model with n classes and unlinked parameters
  --alpha-min NUM      Min Gamma shape parameter for site rates (default: 0.02)
  --gamma-median       Median approximation for +G site rates (default: mean)
  --rate               Write empirical Bayesian site rates to .rate file
  --mlrate             Write maximum likelihood site rates to .mlrate file

POLYMORPHISM AWARE MODELS (PoMo):
  -s FILE              Input counts file (see manual)
  -m ...+P             DNA substitution model (see above) used with PoMo
  -m ...+N<POPSIZE>    Virtual population size (default: 9)
  -m ...+WB|WH|S]      Weighted binomial sampling
  -m ...+WH            Weighted hypergeometric sampling
  -m ...+S             Sampled sampling
  -m ...+G[n]          Discrete Gamma rate with n categories (default n=4)

COMPLEX MODELS:
  -m "MIX{m1,...,mK}"  Mixture model with K components
  -m "FMIX{f1,...fK}"  Frequency mixture model with K components
  --mix-opt            Optimize mixture weights (default: detect)
  -m ...+ASC           Ascertainment bias correction
  --tree-freq FILE     Input tree to infer site frequency model
  --site-freq FILE     Input site frequency model file
  --freq-max           Posterior maximum instead of mean approximation

TREE TOPOLOGY TEST:
  --trees FILE         Set of trees to evaluate log-likelihoods
  --test NUM           Replicates for topology test
  --test-weight        Perform weighted KH and SH tests
  --test-au            Approximately unbiased (AU) test (Shimodaira 2002)
  --sitelh             Write site log-likelihoods to .sitelh file

ANCESTRAL STATE RECONSTRUCTION:
  --ancestral          Ancestral state reconstruction by empirical Bayes
  --asr-min NUM        Min probability of ancestral state (default: equil freq)

TEST OF SYMMETRY:
  --symtest               Perform three tests of symmetry
  --symtest-only          Do --symtest then exist
  --symtest-remove-bad    Do --symtest and remove bad partitions
  --symtest-remove-good   Do --symtest and remove good partitions
  --symtest-type MAR|INT  Use MARginal/INTernal test when removing partitions
  --symtest-pval NUMER    P-value cutoff (default: 0.05)
  --symtest-keep-zero     Keep NAs in the tests

CONCORDANCE FACTOR ANALYSIS:
  -t FILE              Reference tree to assign concordance factor
  --gcf FILE           Set of source trees for gene concordance factor (gCF)
  --df-tree            Write discordant trees associated with gDF1
  --scf NUM            Number of quartets for site concordance factor (sCF)
  --scfl NUM           Like --scf but using likelihood (recommended)
  -s FILE              Sequence alignment for --scf
  -p FILE|DIR          Partition file or directory for --scf
  --cf-verbose         Write CF per tree/locus to cf.stat_tree/_loci
  --cf-quartet         Write sCF for all resampled quartets to .cf.quartet

ALISIM: ALIGNMENT SIMULATOR

Usage: iqtree --alisim <OUTPUT_PREFIX> [-m MODEL] [-t TREE] ...

  --alisim OUTPUT_ALIGNMENT Activate AliSim and specify the output alignment filename
  -t TREE_FILE              Set the input tree file name
  --length LENGTH           Set the length of the root sequence
  --num-alignments NUMBER   Set the number of output datasets
  --seqtype STRING          BIN, DNA, AA, CODON, MORPH{NUM_STATES} (default: auto-detect)
                            For morphological data, 0<NUM_STATES<=32
  --m MODEL_STRING          Specify the evolutionary model. See Manual for more detail
  --mdef FILE               Name of a NEXUS model file to define new models (see Manual)
  --fundi TAXA_LIST,RHO     Specify a list of taxa, and Rho (Fundi weight) for FunDi model
  --indel <INS>,<DEL>       Set the insertion and deletion rate of the indel model,
                            relative to the substitution rate
  --indel-size <INS_DIS>,<DEL_DIS> Set the insertion and deletion size distributions
  --sub-level-mixture       Enable the feature to simulate substitution-level mixture model
  --no-unaligned            Disable outputing a file of unaligned sequences 
                            when using indel models
  --root-seq FILE,SEQ_NAME  Specify the root sequence from an alignment
  -s FILE                   Specify the input sequence alignment
  --no-copy-gaps            Disable copying gaps from input alignment (default: false)
  --site-freq <OPTION>      Specify the option (MEAN (default), or SAMPLING, or MODEL)
                            to mimic the site-frequencies for mixture models from
                            the input alignment (see Manual)
  --site-rate <OPTION>      Specify the option (MEAN (default), or SAMPLING, or MODEL)
                            to mimic the discrete rate heterogeneity from
                            the input alignment (see Manual)
  -t RANDOM{MODEL,NUM_TAXA} Specify the model and the number of taxa to generate a random tree
  -rlen MIN MEAN MAX        Specify three numbers: minimum, mean and maximum branch lengths
                            when generating a random tree
  -p FILE                   NEXUS/RAxML partition file
                            Edge-linked proportional partition model
  -q FILE                   Like -p but edge-linked equal partition model 
  -Q FILE                   Like -p but edge-unlinked partition model
  --distribution FILE       Supply a definition file of distributions,
                            which could be used to generate random model parameters
  --branch-distribution DIS Specify a distribution, from which branch lengths of the input trees
                            are randomly generated and overridden.
  --branch-scale SCALE      Specify a value to scale all branch lengths
  --single-output           Output all alignments into a single file
  --write-all               Enable outputting internal sequences
  --seed NUM                Random seed number (default: CPU clock)
                            Be careful to make the AliSim reproducible,
                            users should specify the seed number
  -gz                       Enable output compression but taking longer running time
  -af phy|fasta             Set the output format (default: phylip)
  User Manual is available at http://www.iqtree.org/doc/alisim

ANALYSIS WITH GENTRIUS ALGORITHM:
  --gentrius FILE      File must contain either a single species-tree or a set of subtrees.
  -pr_ab_matrix FILE   Presence-absence matrix of loci coverage.
  -s FILE              PHYLIP/FASTA/NEXUS/CLUSTAL/MSF alignment file(s)
  -p FILE              NEXUS/RAxML partition file
  -g_stop_t NUM        Stop after NUM species-trees were generated, or use 0 to turn off this stopping rule. Default: 1MLN trees.
  -g_stop_i NUM        Stop after NUM intermediate trees were visited, or use 0 to turn off this stopping rule. Default: 10MLN trees.
  -g_stop_h NUM        Stop after NUM hours (CPU time), or use 0 to turn off this stopping rule. Default: 7 days.
  -g_non_stop          Turn off all stopping rules.
  -g_query FILE        Species-trees to test for identical set of subtrees.
  -g_print             Write all generated species-trees. WARNING: there might be millions of trees!
  -g_print_lim NUM     Limit on the number of species-trees to be written.
  -g_print_induced     Write induced partition subtrees.
  -g_print_m           Write presence-absence matrix.
  -g_rm_leaves NUM     Invoke reverse analysis for complex datasets.

GENOMIC EPIDEMIOLOGICAL ANALYSIS:
  --pathogen           Apply CMAPLE tree search algorithm if sequence
                       divergence is low, otherwise, apply IQ-TREE algorithm.
  --pathogen-force     Apply CMAPLE tree search algorithm regardless
                       of sequence divergence.

TIME TREE RECONSTRUCTION:
  --date FILE          File containing dates of tips or ancestral nodes
  --date TAXNAME       Extract dates from taxon names after last '|'
  --date-tip STRING    Tip dates as a real number or YYYY-MM-DD
  --date-root STRING   Root date as a real number or YYYY-MM-DD
  --date-ci NUM        Number of replicates to compute confidence interval
  --clock-sd NUM       Std-dev for lognormal relaxed clock (default: 0.2)
  --date-no-outgroup   Exclude outgroup from time tree
  --date-outlier NUM   Z-score cutoff to remove outlier tips/nodes (e.g. 3)
  --date-options ".."  Extra options passing directly to LSD2
  --dating STRING      Dating method: LSD for least square dating (default)

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Installation

IQ-Tree

System

64-bit Linux