Build a maximum-likelihood tree with IQ-TREE

Infer a maximum-likelihood phylogeny from an alignment with IQ-TREE 2, using ModelFinder for model selection and 1000 ultrafast bootstraps.

SSSudipta SardarUpdated July 21, 2026

Prerequisites

IQ-TREE 2 installed (`iqtree2` on your PATH)
A multiple sequence alignment in FASTA, PHYLIP, or NEXUS format

1Run ModelFinder with 1000 ultrafast bootstraps

The -m MFP flag runs ModelFinder Plus to pick the best substitution model before tree search, -bb 1000 requests 1000 ultrafast bootstrap replicates, and -nt AUTO lets IQ-TREE benchmark and choose the optimal thread count. The run writes three files prefixed with your alignment name.

bash

iqtree2 -s aligned.fasta -m MFP -bb 1000 -nt AUTO

Expected output

IQ-TREE multicore version 2.2.2.6 for Mac OS X 64-bit built May 27 2023
Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung,
Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams.

Reading alignment file aligned.fasta ... Fasta format detected
Alignment most likely contains DNA/RNA sequences
Alignment has 42 sequences with 1200 columns, 856 distinct patterns

Measuring multi-threading efficiency up to 8 CPU cores
BEST NUMBER OF THREADS: 4

ModelFinder will test up to 286 DNA models (sample size: 1200) ...
 No. Model         -LnL         df  AIC          AICc         BIC
  1  GTR+F+G4      18452.317    89  37082.634    37096.128    37535.492
  ...
Akaike Information Criterion:           GTR+F+G4
Bayesian Information Criterion:         GTR+F+G4
Best-fit model according to BIC: GTR+F+G4

Generating 1000 samples for ultrafast bootstrap (seed: 123456)
BEST SCORE FOUND : -18452.317
Creating bootstrap support values...

Total wall-clock time used: 62.418 sec

Analysis results written to:
  IQ-TREE report:                aligned.fasta.iqtree
  Maximum-likelihood tree:       aligned.fasta.treefile
  Screen log file:               aligned.fasta.log

2Read the bootstrap support values

The .treefile holds the ML tree in Newick format, with ultrafast bootstrap support (0-100) attached to each internal node. Values at or above 95 indicate strongly supported clades; open the tree in FigTree or iTOL for a visual view.

bash

cat aligned.fasta.treefile

Expected output

(SeqA:0.0123,(SeqB:0.0210,SeqC:0.0187)98:0.0056,((SeqD:0.0301,SeqE:0.0278)100:0.0142,SeqF:0.0256)87:0.0091);

Troubleshooting

The number of bootstrap replicates must be >= 1000

Ultrafast bootstrap (`-bb`) requires at least 1000 replicates. Set `-bb 1000` or higher; use `-b` instead for standard nonparametric bootstrap with fewer replicates.

IQ-TREE warns that some sequences are identical and drops them

This is expected, not an error. IQ-TREE removes duplicate/identical sequences to speed up the search and lists them in the .log; add them back onto the tree manually if you need every taxon shown.

References

IQ-TREE documentation