IQ-Tree-Teaching
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Category
Bioinformatics
Program On
Teaching
Version
1.5.5, 1.6.5
Author / Distributor
Please see http://www.iqtree.org/
Description
Efficient phylogenomic software by maximum likelihood. More information: http://www.iqtree.org/
Running Program
- Version 1.5.5, installed in /usr/local/apps/eb/IQ-TREE/1.5.5-foss-2016b-omp-mpi
To use this version of IQ-TREE, please first load the module with
module load IQ-TREE/1.5.5-foss-2016b-omp-mpi
- Version 1.6.5, installed in /usr/local/apps/eb/IQ-TREE/1.6.5-omp
To use this version of IQ-TREE, please first load the module with
module load IQ-TREE/1.6.5-omp
Sample job submission script (sub.sh) to run IQ-Tree version. 1.6.5:
#!/bin/bash
#SBATCH --job-name=j_BEDTools
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=HTSeq.%j.out
#SBATCH --error=HTSeq.%j.err
cd $SLURM_SUBMIT_DIR
module load IQ-TREE/1.6.5-omp
iqtree [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/1.6.5-omp
iqtree -h
IQ-TREE multicore version 1.6.5 for Linux 64-bit built May 8 2018
Developed by Bui Quang Minh, Nguyen Lam Tung, Olga Chernomor,
Heiko Schmidt, Dominik Schrempf, Michael Woodhams.
Usage: iqtree -s <alignment> [OPTIONS]
GENERAL OPTIONS:
-? or -h Print this help dialog
-version Display version number
-s <alignment> Input alignment in PHYLIP/FASTA/NEXUS/CLUSTAL/MSF format
-st <data_type> BIN, DNA, AA, NT2AA, CODON, MORPH (default: auto-detect)
-q <partition_file> Edge-linked partition model (file in NEXUS/RAxML format)
-spp <partition_file> Like -q option but allowing partition-specific rates
-sp <partition_file> Edge-unlinked partition model (like -M option of RAxML)
-t <start_tree_file> or -t BIONJ or -t RANDOM
Starting tree (default: 99 parsimony tree and BIONJ)
-te <user_tree_file> Like -t but fixing user tree (no tree search performed)
-o <outgroup_taxon> Outgroup taxon name for writing .treefile
-pre <PREFIX> Prefix for all output files (default: aln/partition)
-nt <num_threads> Number of cores/threads or AUTO for automatic detection
-ntmax <max_threads> Max number of threads by -nt AUTO (default: #CPU cores)
-seed <number> Random seed number, normally used for debugging purpose
-v, -vv, -vvv Verbose mode, printing more messages to screen
-quiet Quiet mode, suppress printing to screen (stdout)
-keep-ident Keep identical sequences (default: remove & finally add)
-safe Safe likelihood kernel to avoid numerical underflow
-mem RAM Maximal RAM usage for memory saving mode
--runs NUMBER Number of indepedent runs (default: 1)
CHECKPOINTING TO RESUME STOPPED RUN:
-redo Redo analysis even for successful runs (default: resume)
-cptime <seconds> Minimum checkpoint time interval (default: 60 sec)
LIKELIHOOD MAPPING ANALYSIS:
-lmap <#quartets> Number of quartets for likelihood mapping analysis
-lmclust <clustfile> NEXUS file containing clusters for likelihood mapping
-wql Print quartet log-likelihoods to .quartetlh file
NEW STOCHASTIC TREE SEARCH ALGORITHM:
-ninit <number> Number of initial parsimony trees (default: 100)
-ntop <number> Number of top initial trees (default: 20)
-nbest <number> Number of best trees retained during search (defaut: 5)
-n <#iterations> Fix number of iterations to stop (default: auto)
-nstop <number> Number of unsuccessful iterations to stop (default: 100)
-pers <proportion> Perturbation strength for randomized NNI (default: 0.5)
-sprrad <number> Radius for parsimony SPR search (default: 6)
-allnni Perform more thorough NNI search (default: off)
-g <constraint_tree> (Multifurcating) topological constraint tree file
-fast Fast search to resemble FastTree
ULTRAFAST BOOTSTRAP:
-bb <#replicates> Ultrafast bootstrap (>=1000)
-bsam GENE|GENESITE Resample GENE or GENE+SITE for partition (default: SITE)
-wbt Write bootstrap trees to .ufboot file (default: none)
-wbtl Like -wbt but also writing branch lengths
-nm <#iterations> Maximum number of iterations (default: 1000)
-nstep <#iterations> #Iterations for UFBoot stopping rule (default: 100)
-bcor <min_corr> Minimum correlation coefficient (default: 0.99)
-beps <epsilon> RELL epsilon to break tie (default: 0.5)
-bnni Optimize UFBoot trees by NNI on bootstrap alignment
-j <jackknife> Proportion of sites for jackknife (default: NONE)
STANDARD NON-PARAMETRIC BOOTSTRAP:
-b <#replicates> Bootstrap + ML tree + consensus tree (>=100)
-bc <#replicates> Bootstrap + consensus tree
-bo <#replicates> Bootstrap only
SINGLE BRANCH TEST:
-alrt <#replicates> SH-like approximate likelihood ratio test (SH-aLRT)
-alrt 0 Parametric aLRT test (Anisimova and Gascuel 2006)
-abayes approximate Bayes test (Anisimova et al. 2011)
-lbp <#replicates> 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 TESTMERGEONLY Find best partition scheme (like PartitionFinder)
-m TESTMERGE Find best partition scheme followed by tree inference
-m MF+MERGE Find best partition scheme incl. FreeRate heterogeneity
-m MFP+MERGE Like -m MF+MERGE followed by tree inference
-rcluster <percent> Percentage of partition pairs (relaxed clustering alg.)
-rclusterf <perc.> Percentage of partition pairs (fast relaxed clustering)
-rcluster-max <num> Max number of partition pairs (default: 10*#partitions)
-mset program Restrict search to models supported by other programs
(raxml, phyml or mrbayes)
-mset <lm-subset> Restrict search to a subset of the Lie-Markov models
Options for lm-subset are:
liemarkov, liemarkovry, liemarkovws, liemarkovmk, strandsymmetric
-mset m1,...,mk Restrict search to models in a comma-separated list
(e.g. -mset WAG,LG,JTT)
-msub source Restrict search to AA models for specific sources
(nuclear, mitochondrial, chloroplast or viral)
-mfreq f1,...,fk Restrict search to using a list of state frequencies
(default AA: -mfreq FU,F; codon: -mfreq ,F1x4,F3x4,F)
-mrate r1,...,rk Restrict search to a list of rate-across-sites models
(e.g. -mrate E,I,G,I+G,R is used for -m MF)
-cmin <kmin> Min #categories for FreeRate model [+R] (default: 2)
-cmax <kmax> Max #categories for FreeRate model [+R] (default: 10)
-merit AIC|AICc|BIC Optimality criterion to use (default: all)
-mtree Perform full tree search for each model considered
-mredo Ignore model results computed earlier (default: reuse)
-madd mx1,...,mxk List of mixture models to also consider
-mdef <nexus_file> A model definition NEXUS file (see Manual)
SUBSTITUTION MODEL:
-m <model_name>
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
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: One of the following, optionally prefixed by RY, WS or MK:
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
Non-reversible: STRSYM (strand symmetric model, synonymous with WS6.6)
Non-reversible: UNREST (most general unrestricted model, functionally equivalent to 12.12)
Models can have parameters appended in brackets.
e.g. '-mRY3.4{0.2,-0.3}+I' specifies parameters for
RY3.4 model but leaves proportion of invariant sites
unspecified. '-mRY3.4{0.2,-0.3}+I{0.5} gives both.
When this is done, the given parameters will be taken
as fixed (default) or as start point for optimization
(if -optfromgiven option supplied)
Otherwise: Name of file containing user-model parameters
(rate parameters and state frequencies)
STATE FREQUENCY:
Append one of the following +F... to -m <model_name>
+F Empirically counted frequencies from alignment
+FO (letter-O) Optimized frequencies by maximum-likelihood
+FQ Equal frequencies
+FRY, +FWS, +FMK For DNA models only, +FRY is freq(A+G)=1/2=freq(C+T),
+FWS is freq(A+T)=1/2=freq(C+G), +FMK is freq(A+C)=1/2=freq(G+T).
+F#### where # are digits - for DNA models only, for basis in ACGT order,
digits indicate which frequencies are constrained to be the same.
E.g. +F1221 means freq(A)=freq(T), freq(C)=freq(G).
+FU Amino-acid frequencies by the given protein matrix
+F1x4 (codon model) Equal NT frequencies over three codon positions
+F3x4 (codon model) Unequal NT frequencies over three codon positions
MIXTURE MODEL:
-m "MIX{model1,...,modelK}" Mixture model with K components
-m "FMIX{freq1,...freqK}" Frequency mixture model with K components
-mwopt Turn on optimizing mixture weights (default: none)
RATE HETEROGENEITY AMONG SITES:
-m modelname+I A proportion of invariable sites
-m modelname+G[n] Discrete Gamma model with n categories (default n=4)
-m modelname*G[n] Discrete Gamma model with unlinked model parameters
-m modelname+I+G[n] Invariable sites plus Gamma model with n categories
-m modelname+R[n] FreeRate model with n categories (default n=4)
-m modelname*R[n] FreeRate model with unlinked model parameters
-m modelname+I+R[n] Invariable sites plus FreeRate model with n categories
-m modelname+Hn Heterotachy model with n classes
-m modelname*Hn Heterotachy model with n classes and unlinked parameters
-a <Gamma_shape> Gamma shape parameter for site rates (default: estimate)
-amin <min_shape> Min Gamma shape parameter for site rates (default: 0.02)
-gmedian Median approximation for +G site rates (default: mean)
--opt-gamma-inv More thorough estimation for +I+G model parameters
-i <p_invar> Proportion of invariable sites (default: estimate)
-wsr Write site rates to .rate file
-mh Computing site-specific rates to .mhrate file using
Meyer & von Haeseler (2003) method
POLYMORPHISM AWARE MODELS (PoMo):
-s <counts_file> Input counts file (see manual)
-m <MODEL>+P DNA substitution model (see above) used with PoMo
+N<POPSIZE> Virtual population size (default: 9)
+[WB|WH|S] Sampling method (default: +WB), WB: Weighted binomial,
WH: Weighted hypergeometric S: Sampled sampling
+G[n] Discrete Gamma rate model with n categories (default n=4)
ASCERTAINMENT BIAS CORRECTION:
-m modelname+ASC Correction for absence of invariant sites in alignment
SINGLE TOPOLOGY HETEROTACHY MODEL:
-m <model_name>+H[k] Heterotachy model mixed branch lengths with k classes
-m "MIX{m1,...mK}+H"
-nni-eval <m> Loop m times for NNI evaluation (default m=1)
SITE-SPECIFIC FREQUENCY MODEL:
-ft <tree_file> Input tree to infer site frequency model
-fs <in_freq_file> Input site frequency model file
-fmax Posterior maximum instead of mean approximation
CONSENSUS RECONSTRUCTION:
-t <tree_file> Set of input trees for consensus reconstruction
-minsup <threshold> Min split support in range [0,1]; 0.5 for majority-rule
consensus (default: 0, i.e. extended consensus)
-bi <burnin> Discarding <burnin> trees at beginning of <treefile>
-con Computing consensus tree to .contree file
-net Computing consensus network to .nex file
-sup <target_tree> Assigning support values for <target_tree> to .suptree
-suptag <name> Node name (or ALL) to assign tree IDs where node occurs
ROBINSON-FOULDS DISTANCE:
-rf_all Computing all-to-all RF distances of trees in <treefile>
-rf <treefile2> Computing all RF distances between two sets of trees
stored in <treefile> and <treefile2>
-rf_adj Computing RF distances of adjacent trees in <treefile>
TREE TOPOLOGY TEST:
-z <trees_file> Evaluating a set of user trees
-zb <#replicates> Performing BP,KH,SH,ELW tests for trees passed via -z
-zw Also performing weighted-KH and weighted-SH tests
-au Also performing approximately unbiased (AU) test
ANCESTRAL STATE RECONSTRUCTION:
-asr Ancestral state reconstruction by empirical Bayes
-asr-min <prob> Min probability of ancestral state (default: equil freq)
GENERATING RANDOM TREES:
-r <num_taxa> Create a random tree under Yule-Harding model
-ru <num_taxa> Create a random tree under Uniform model
-rcat <num_taxa> Create a random caterpillar tree
-rbal <num_taxa> Create a random balanced tree
-rcsg <num_taxa> Create a random circular split network
-rlen <min_len> <mean_len> <max_len>
min, mean, and max branch lengths of random trees
MISCELLANEOUS:
-wt Write locally optimal trees into .treels file
-blfix Fix branch lengths of user tree passed via -te
-blscale Scale branch lengths of user tree passed via -t
-blmin Min branch length for optimization (default 0.000001)
-blmax Max branch length for optimization (default 100)
-wsr Write site rates and categories to .rate file
-wsl Write site log-likelihoods to .sitelh file
-wslr Write site log-likelihoods per rate category
-wslm Write site log-likelihoods per mixture class
-wslmr Write site log-likelihoods per mixture+rate class
-wspr Write site probabilities per rate category
-wspm Write site probabilities per mixture class
-wspmr Write site probabilities per mixture+rate class
-wpl Write partition log-likelihoods to .partlh file
-fconst f1,...,fN Add constant patterns into alignment (N=#nstates)
-me <epsilon> LogL epsilon for parameter estimation (default 0.01)
--no-outfiles Suppress printing output files
--eigenlib Use Eigen3 library
-alninfo Print alignment sites statistics to .alninfo
-czb Collapse zero branches in final tree
--show-lh Compute tree likelihood without optimisation
Installation
System
64-bit Linux