IQ-TREE version 1.0.0

Jul 28, 2014

We are happy to announce the major release of IQ-TREE software version 1.0.0 with the following news:

Integration of the phylogenetic likelihood library for fast likelihood computation. This is enabled via -pll option and gives a speedup of 2X to 8X.
A novel fast and effective stochastic algorithm for estimating maximum likelihood phylogenies. It outperforms RAxML and PhyML in terms of log-likelihoods while requiring similar amount of computing time. A manuscript describing the new method was submitted.
NEW MODELS: codon models and ascertainment bias correction model for morphological or single-nucleotide-polymorphism (SNP) data.
Nearest neighbor interchange with five branch optimization (-nni5) is now the default option because of its higher accuracy.
SH-aLRT branch test also works now for partition models.