IQ-Tree-Teaching
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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)
Installation
System
64-bit Linux