| PackageDescription | 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) |