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)