In contrast, when unrelated alignments were merged (first half of alignment #1 with the second half of alignment #2 etc), all log likelihoods from combined alignments were substantially lower than the sum of individual log likelihoods (difference ranged from -133 to -45 log likelihood units with the mean of -90).
Training sets ranging from 50 to 50,000 read-half alignments were used to train the HMM with two different sets of initial HMM values.
The HMM is trained on a subset of read-half alignments to best reflect the quality and base composition of the dataset and genome.
Even for these four cases, the new results exhibit considerable similarity to the original alignments (half or more of the aligned NCIVs are the same).
The upper half shows the alignment of the five different human B56 isoforms, whereas the lower half demonstrates the sequence conservation of B56γ from different organisms.
An average posterior probability of 0.5 could be the result of an uncertain reconstruction (PP of 0.5 for the sites' true tree) at all sites, or it could be the result of a perfect reconstruction (PP of 1.0 for the sites' true tree) along half of the alignment and an very incorrect reconstruction (PP of 0.0 for the sites' true tree) along the other half of the alignment.
Likewise, the MLBP support for the T. globosa + discicristates clade was greater than for a T. globosa + jakobids group or for T. globosa occupying the most basal position in the Discoba clade until more than half of the alignment positions in the original data set were excluded (fig. 2 A).
Two models best describe evolution in over half of the alignments, our new 7G model, the simplest of the Stable Pairs set, and the most complex Stable Sets model, 16D.
North of Copake Falls, the northern half of the original alignment was designated as an extension of NY 344.
Route 153 was deleted from the Regional Transportation Plan starting in May 2007, and much of the western half of the original alignment was re-used as right-of-way for the Sky Train people mover at Phoenix Sky Harbor International Airport.
To investigate this effect in bulk we compared amino acid and nucleotide changes between LT orthologs and LL paralogs over an alignment of half a million amino acids.
