The Gaussian Mixture model (GM) (Day, 1969; Wolfe, 1970; McLachlan and Basford, 1988) or mixture maximum-likelihood method
(or Normix) has been used to classify into g homogeneous subpopulations a random sample of n observations [x.sub.1], [x.sub.2], ...
Molecular phylogenetic analysis by maximum-likelihood method
of isolates from a patient in Germany with recurrent fever episodes after traveling to southern Africa, 2015.
Below we describe, after introducing a maximum-likelihood method
for estimating population divergence times, a statistical population genetic approach to the inference of population phylogeny.
We constructed a phylogenetic tree of N and F gene segments from a representative selection of PPRV sequences available in GenBank, using the maximum-likelihood method
available in MEGA6 (https://www.megasoftware.
Using sequences from both regions, we inferred phylogenetic trees by the maximum-likelihood method
as implemented in MEGA 6.0 (8).
Here we describe a maximum-likelihood method
for estimating selection coefficients for continuously varying phenotypic traits from capture-recapture data.
For Bartonella spp., sequence of the ITS-1 fragment amplified by standard PCR and phylogenetic analysis with maximum-likelihood method
and 1,000 bootstrap replicates, performed using MEGA software version 6 (5), confirmed the bacteria as B.
The tree was created by using the maximum-likelihood method
based on the Kimura 2-parameter model with 500 bootstrap replicates from the whole-genome sequence of the displayed sequences.
Phylogenetic trees of the individual segments were inferred by using the maximum-likelihood method
implemented in the IQ-TREE package 0.9.6 (8).
The analysis was carried out by using the maximum-likelihood method
in MEGA 5.0 (10), and the reliability of tree topology was evaluated through bootstrapping with 1,000 replicates.
Phylogenetic trees were constructed by using MEGA5 (10) with the maximum-likelihood method
and the Jukes-Cantor algorithm with 500 bootstrap replicates.
Because of absence of entire sequences from strains that co-circulated in South Africa and Namibia in 2009-2010, we performed phylogenetic analysis of a 490-nt fragment by using a selection of reference strains that had been isolated in different years or countries (online Technical Appendix Table 3) using the maximum-likelihood method
in MEGA version 5 (14) with bootstrap support (1,000 replicates) (online Technical Appendix Figure 2).