IQ-Tree-Sapelo2
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Category
Bioinformatics
Program On
Sapelo2
Version
1.6.12, 2.2.2.6
Author / Distributor
Please see http://www.iqtree.org/
Description
Efficient phylogenomic software by maximum likelihood. More information: http://www.iqtree.org/
Running Program
- Version 2.2.2.6, installed in /apps/eb/IQ-TREE/2.2.2.6-gompi-2022a
To use this version of IQ-TREE, please first load the module with
module load IQ-TREE/2.2.2.6-gompi-2022a
- Version 1.6.12, installed in /apps/eb/IQ-TREE/1.6-12-foss-2019b
To use this version of IQ-TREE, please first load the module with
module load IQ-TREE/1.6.12-foss-2019b
Sample job submission script (sub.sh) to run IQ-Tree version. 1.6.12:
#!/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/1.6.12-foss-2019b
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 Sapelo2 for more information on running jobs on the Sapelo2 cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
module load IQ-TREE/1.6.12-foss-2019b
iqtree -h
IQ-TREE multicore version 1.6.12 for Linux 64-bit built Jul 9 2020
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