Sentence examples for alignment were calculated using from inspiring English sources

Plots of sequence similarity along the alignment were calculated using the program plotcon from EMBOSS (Rice et al. 2000).

The distances between 5' and 3' LTR sequences for each alignment were calculated using the Kimura 2-parameter distmat tool from EMBOSS package [ 63].

The per-site likelihoods of the 16S topology and the topology based on the butyrate kinase alignment were calculated using FastTree with the butyrate kinase alignment as the data set, and an approximately unbiased (AU) test was performed using CONSEL (Shimodaira and Hasegawa 2001).

Structural alignment was calculated using TM-align program [ 29] as implemented in T-Coffee package [ 30].

A score for each column in the alignment is calculated using the concept of continuous sequence space introduced by Vingron and Sibbald [64] and the column scores are then summed over the full length of the alignment.

The optimal structure element alignment is calculated using dynamic programming.

For each family, a multiple sequence alignment was calculated using POA [ 56].

The conservation degree of the alignment was calculated using PLOTCON (31).

A structure-based multiple sequence alignment was calculated using Expresso (3DCoffee) (Armougom et al., 2006).

The CIGAR string of the BLAT alignment is calculated using the method proposed by Heng Li (https://github.com/lh3/samtools-legacy/blob/master/misc/psl2sam.pl).

The variability in each column of the multiple sequence alignment is calculated using the Shannon entropy (H) function.