iqtree
efficient phylogenetic software by maximum likelihood
Install
- All systems
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curl cmd.cat/iqtree.sh
- Debian
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apt-get install iqtree - Ubuntu
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apt-get install iqtree - Kali Linux
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apt-get install iqtree - Windows (WSL2)
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sudo apt-get updatesudo apt-get install iqtree - Dockerfile
- dockerfile.run/iqtree
iqtree
efficient phylogenetic software by maximum likelihood
IQ-TREE is a very efficient maximum likelihood phylogenetic software with following key features among others: * A novel fast and effective stochastic algorithm to estimate maximum likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms of likelihood while requiring similar amount of computing time (see Nguyen et al., 2015) * An ultrafast bootstrap approximation to assess branch supports (see Minh et al., 2013). * A wide range of substitution models for binary, DNA, protein, codon, and morphological alignments. * Ultrafast model selection for all data types, 10 to 100 times faster than jModelTest and ProtTest. * Finding best partition scheme like PartitionFinder. * Partitioned models with mixed data types for phylogenomic (multi- gene) alignments, allowing for separate, proportional, or joint branch lengths among genes. * Supporting the phylogenetic likelihod library (PLL) (see Flouri et al., 2014)