Sentence examples for alignment estimates from inspiring English sources

We used default parameters for all alignment estimates.

For each amino acid site in the alignment, estimates of the number of synonymous and non-synonymous sites were calculated for a given part of the tree as follows: S s = 1 V T ∑ i = 1 c ∑ j = 1 3 s ij v ij S n = 1 V T ∑ i = 1 c ∑ j = 1 3 n ij v ij where c = number of codon intervals (distinct codon states) along a part of the tree.

The choice of a fixed alignment estimate is indicated in column  if applicable.

Inspecting the alignment estimate from the MAP point using a "gold" plot demonstrates alignment uncertainty (data not shown).

The PDM method scans the entire alignment, estimating phylogenies for fixed sequence windows with a Markov Chain Monte Carlo process.

Joint estimation of alignment and phylogeny sidesteps bias that results from conditioning on a single alignment estimate [ 21, 18], bias which may be exaggerated when indel information is inappropriately used.

We note that in one column of the singlet MAP alignment estimate, only variants 10, 12 and 18 have an A residue, while other taxa have either a G residue or a gap.

See File S1. S. cerevisiae and S. paradoxus gene sequences from SGRP strains (Liti et al. 2009) were downloaded from http://www.moseslab.csb.utoronto.ca/sgrp/blast_original. Sequence alignment, estimating maximum likelihood tree (1,000 permutations) and Tajima's D were done using MEGA 6.06 (Tamura et al. 2013).

Using these alignments, estimate the distribution of fragment lengths.

Sequence alignments estimated that the smallest A-tail was 13 bp and the largest was 62 bp, with an average length of approximately 29 bp.

Second, the divide-and-conquer approach used in DACTAL produces small densely sampled subsets containing sequences that tend to be very similar; these features increase the accuracy of estimated alignments, so that ML trees computed on these subset alignments tend to be more accurate than ML trees computed on alignments estimated on the full dataset.