IQ-Tree-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

2.2.2.7, 2.3.5, 2.3.6

Author / Distributor

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

Description

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

Running Program

• Version 2.2.2.7, installed in /apps/eb/IQ-TREE/2.2.2.7-gompi-2023a

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

module load IQ-TREE/2.2.2.7-gompi-2023a

• Version 2.3.5, installed in /apps/eb/IQ-TREE/2.3.5-gompi-2023a

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

module load IQ-TREE/2.3.5-gompi-2023a

• 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

Please note: The name of the executable for IQ-TREE version 2+ is iqtree2 and iqtree2-mpi (MPI version).

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 --cpus-per-task=4
#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. If you request multiple cores per tasks in order to have iqtree2 run with multiple threads, then please use the -T option to specify how many threads iqtree2 should use. We recommend setting the number of threads to match the number of cores requested, e.g. -T 4 in this example.

Please refer to Running Jobs on Sapelo2 for more information on running jobs on the Sapelo2 cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

[shtsai@b1-24 ~]$ ml IQ-TREE/2.3.6-gompi-2023a
[shtsai@b1-24 ~]$ 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