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The stack was subjected to reference-free maximum likelihood alignment.
(C ) Initial class averages obtained by reference-free maximum likelihood alignment and classification.
Then for each gene segment, the maximum likelihood alignment between it and A Q is computed.
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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All VH segments with equally high likelihood alignments are then submitted to the HMM.
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).
To reduce the likelihood of alignment artifacts as a result of ambiguities, only the commonly predicted alignments from the two programs were used in further analyses.
From two different analyses of genes up-regulated in the Igf1−/− cochlea a possible binding site for the MEF2 transcription factor was identified with the strongest likelihood of alignment.
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