iqtree

efficient phylogenetic software by maximum likelihood

Description

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)

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