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The reads were realigned using the local realignment tool in Strand NGS.

In brief, reads containing indels were realigned using the Smith-Waterman algorithm (by GATK RealignerTargetCreator and Indel Realigner).

Predicted indels were realigned using a Smith Waterman approach21.

The k 2, V A, and V RV images were realigned using the same transforms.

All images from a single subject were realigned using a 6-parameter rigid body process, replaced by a cubic spline interpolation.

Data were realigned using the INRIAlign [31] toolbox.

The repaired version of cd00300 was realigned using Cn3D [22] based on a refined structure alignment based on errors of probable misalignment according to increased local covariance.

In the second experiment, the sequences with discrepancies were excluded from the benchmark test sets and each sequence set was realigned using the eight MSA programs.The quality of the resulting alignments was again measured using the CS score (Figure 5).

Subsequently, each pair of orthologous sequences was realigned using cmalign (Nawrocki et al. 2009).

The resultant subgroup was realigned using T-COFFEE and visually inspected and altered for corrections.

The postoperative imaging time series of each subject was realigned using the mean image as a reference.