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The stack was subjected to reference-free maximum likelihood alignment.
Then for each gene segment, the maximum likelihood alignment between it and A Q is computed.
(C ) Initial class averages obtained by reference-free maximum likelihood alignment and classification.
Classes were obtained by reference-free maximum likelihood alignment and classification and are sorted by Group.
A combined stack of 70,000 particles (10,000 particles from each strain) was subjected to reference-free maximum likelihood alignment.
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Maximum likelihood alignments are generated with an initial global alignment by dynamic programming followed by dynamic local alignments.
Maximum likelihood alignments are generated with an initial global alignment by dynamic programming [ 36- 38] followed by dynamic local alignments [ 39].
Maximum likelihood alignments are generated with an initial global alignment by dynamic programming (Smith and Waterman algorithm) followed by dynamic local alignments (Needleman and Wunsch algorithm).
For the construction of phylogenetic trees by the Neighbor Joining Method and the Maximum Likelihood Method, alignment gaps were disregarded when more than 95% of the sequences were non-informative in this position.
To obtain appropriate substitution models for maximum likelihood analysis, each alignment was analysed with Modeltest 3.6 [ 57] using the Akaike information criterion in its AICc variant [ 58].
The models can be represented as follows: The LRT statistic for block B is where the parameters γ and ρ are estimated for each model by maximum likelihood, using the alignment data for block B. The null hypothesis being tested is H0: ρ = 1 (no acceleration in Hominini) versus the alternative hypothesis Ha: ρ > 1 (acceleration in Hominini).
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maximum likelihood reconstruction
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maximum likelihood learning
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maximum likelihood Estimation
maximum accuracy alignment
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maximum likelihood phylogram
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