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We align the projection images according to the various alignment methods, and each realigned set of projections is reconstructed again using TV minimization.
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To measure the intra-rater reliability, the same author who manually word aligned the training sets and test sets, MN, realigned the test sets one month after the first alignment.
These sequences were then extracted and realigned to the set of D. melanogaster TEs to determine the TE family to which they were most similar.
We then realigned a final set of 230 ITS, 5.8S and D1/D2 sequences using the FFT-NS-i strategy of MAFFT (dataset 2).
In a second step, we realigned the DTI set which simultaneously corrects for gradient-induced distortions and head movement (Andersson and Skare 2002).
Realign the reads set to the MT+NUMTs database as single-end reads by BWA with the option '-n 10000' (to make sure the result shows all possible hits).
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).
The only way to straighten them would be to perform osteotomies on them, which involves breaking the bones under general anaesthesia, then realigning the fractures so they set in a straight line.
Data sets were realigned and new phylogenetic analyses were carried out.
To assess the assembly quality, all read sets were realigned on the contigs and had an alignment rate of at least 80%.
The reduced data sets were realigned using MAFFT (Katoh et al. 2002), and sites with ambiguous alignments were removed by the Gblocks method in SEAVIEW software (Gouy et al. 2010) with options for a less stringent selection: allow smaller final blocks; allow gap positions within the final blocks; and allow less strict flanking positions.
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