Maximum Likelihood
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PoissonMax v.2.8
PoissonMax is a handy, small, command prompt based application specially designed to compute Poisson maximum likelihood mean frequency from limiting dilution data, with 95% confidence limits and Chi-square value.
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STEM (Species Tree Estimation using Maximum) v.1.1
STEM (Species Tree Estimation using Maximum) is is a software for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model.
Malin v.1.0
Malin (Maximum Likelihood Analysis of Intron Evolution) is a utility package for the analysis of eukaryotic gene structure evolution.
FastTree v.2.1.3
Phylogenetic trees analysis made easy. FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
Phylo_win v.2.0
Molecular phylogenetic inference made easy. Phylo_win is a graphical colour interface for molecular phylogenetic inference. It performs neighbor-joining, parsimony and maximum likelihood methods and bootstrap with any of them.
SEMPHY v.2.0 Beta 1
SEMPHY is a software for data-intensive phylogenetic reconstruction. It infers phylogenies by Maximum Likelihood, the most established criterion for finding the correct phylogenetic tree. SEMPHY searches for both the most likely topology of the
UNPHASED v.3.1.5
UNPHASED is an software for performing genetic association analysis in nuclear families and unrelated subjects. It implements maximum-likelihood inference on haplotype and genotype effects while allowing for uncertain phase and missing genotypes.
SSA v.1.0
SSA is a software for inferring maximum likelihood phylogenies from DNA sequences. Two versions of the software are available: one which assumes a molecular clock and one which does not make this assumption. The method for searching the space of
MLtree v.1.0
Likelihood estimation of model parameters made easy. MLtree implement maximum likelihood estimation of model parameters given a fixed topology with user-defined branch lengths.
Leaphy v.1.0 Beta
Likelihood estimation algorithms in phylogenetics. Leaphy uses maximum likelihood (ML) to estimate trees from aligned amino acid and nucleotide sequences under a variety of commonly used and popular models.The 1.
LAPD v.1.0
LAPD can estimate maximum likelihood allele. LAPD is a convenient, easy-to-use software specially designed to enable you to estimate maximum likelihood allele and two-locus haplotype frequencies, using an Expectation-Maximization algorithm,