Efficient phylogenomic software by maximum likelihood
Efficient and versatile phylogenomic software by maximum likelihood http://www.iqtree.org
The IQ-TREE software was created as the successor of IQPNNI and TREE-PUZZLE (thus the name IQ-TREE). IQ-TREE was motivated by the rapid accumulation of phylogenomic data, leading to a need for efficient phylogenomic software that can handle a large amount of data and provide more complex models of sequence evolution. To this end, IQ-TREE can utilize multicore computers and distributed parallel computing to speed up the analysis. IQ-TREE automatically performs checkpointing to resume an interrupted analysis.
As input IQ-TREE accepts all common sequence alignment formats including PHYLIP, FASTA, Nexus, Clustal and MSF. As output IQ-TREE will write a self-readable report file (name suffix .iqtree
), a NEWICK tree file (.treefile
) which can be visualized by tree viewer programs such as FigTree, Dendroscope or iTOL.
The strength of IQ-TREE is the availability of a wide variety of phylogenetic models:
For a quick start you can also try the IQ-TREE web server, which performs online computation using a dedicated computing cluster. It is very easy to use with as few as just 3 clicks! Try it out at
http://iqtree.cibiv.univie.ac.at
Please refer to the user documentation and frequently asked questions. If you have further questions, feedback, feature requests, and bug reports, please sign up the following Google group (if not done yet) and post a topic to the
https://groups.google.com/d/forum/iqtree
The average response time is one working day.
When using ModelFinder please cite:
When performing tree reconstruction please cite:
For the ultrafast bootstrap (UFBoot) please cite:
When using posterior mean site frequency model (PMSF) please cite:
When using partition models please cite:
When using polymorphism-aware models please cite:
Some parts of the code were taken from the following packages/libraries: Phylogenetic likelihood library, TREE-PUZZLE, BIONJ, Nexus Class Libary, Eigen library, SPRNG library, Zlib library, gzstream library, vectorclass library, GNU scientific library.
IQ-TREE was partially funded by the Austrian Science Fund - FWF (grant no. I 760-B17 from 2012-2015 and and I 2508-B29 from 2016-2019) and the University of Vienna (Initiativkolleg I059-N).