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That afternoon, Eli Lief, a 16-year-old from the East Village, dropped by for help with an oscillator, which he was using to align a tape machine.
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First, a sequence aligner is used to align the reads to the reference genome.
ClustalW [ 176] and Treeview software [ 177] were used to align sequences and visualise alignments.
ClustalW [ 91] and TreeView software [ 92] were used to align sequences and visualize alignments.
Unspliced aligners may be used to align reads to a reference transcriptome or a reference genome.
The protein alignments were then used to align the nucleotide sequences in MacClade 4.5.
The MEGA 5 ClustalW multiple alignment algorithm was used to align all 102 sequences [ 36].
T-COFFEE version 8.93 [99] was used to align amino acid sequences and aa alignments were used as a template to align the corresponding codons.
Multiple sequence alignment program, CLUSTALW has been used to align kinase domain sequences from each of the 72 clusters [124].
Progressive alignment is the standard approach used to align large numbers of sequences.
Similarly, advanced graph alignment algorithms, such as IsoRankN [55] may be used to align DCNs for phylogeny inference.
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