Sentence examples for alignment was estimated from inspiring English sources
The number of amino acid replacements per sequence position in the alignment was estimated using the JTT model [ 66].
The best fitting model according to the corrected Akaike Information Criterion for each alignment was estimated for exon and intron sequences separately with MrModeltest v. 2.3 [ 60].
The coverage of the alignment was estimated and the over-low/high covered sites were discarded by a custom made script to avoid incorrect mapping introduced by random factors or piling up of reads from duplicated genomic regions.
For the paralinear distance analyses, the proportion of invariable sites in the considered alignment was estimated using likelihood and assuming a HKY85 + gamma + proportion of invariable sites model of DNA evolution.
The expected number of substitutions in an alignment was estimated as alignment length multiplied by the fraction of nonidentical bases (the expected number in a bin was found by summing over all bin alignments).
A multiple sequence alignment was estimated using MUSCLE (Edgar, 2004) with MAXITERS set to 2, followed by the removal of identical sequences and the deletion of columns in which the seed had a gap.
The total sight distance deficiency of an alternative alignment is estimated based on (i) the length of the road segments where ASD < SSD and (ii) the significance of sight distance restriction.
The affine transformation parameters to bring the images into global alignment were estimated and used to initialize the local registration step.
The most popular such techniques are summary methods, in which an alignment is estimated on each locus, a gene tree is estimated on each alignment, and then the resulting gene trees are combined into a species tree.
The Akirin1 and Akirin2 clades were defined as separate clusters and the coefficient of functional divergence and posterior probability for functional divergence at each site in the alignment were estimated using the Gu99 algorithm [ 28].
The probability of finding in random networks two nodes with the same or higher interaction overlap as a given alignment is estimated, and serves as a p-value for the corresponding alignment [See Additional file 1 for details.] We use an iterative algorithm as described in [ 7] to find the high-scoring graph alignments.
