Disadvantages of both treatment options for alignment of impacted canines into the dental arch are a long treatment time and high costs, not to mention the unpredictable final outcome [2, 9, 10].
Because MotIV uses the STAMP source code, it provides a range of options for alignment calculations (see the documentation for the R package and/or STAMP).
The Metabolomics Toolbox has several options for alignment, but we found that the star alignment algorithm where an individual spectrum is chosen as a "star" to which all other spectra are aligned, gave the best results in this study.
The input to the program is simple and consists of two FASTA files, e.g. reference sequence and assembled contig, specification of expected SV, e.g. option –inv for alignment with inversions, and optional specification of sequence subranges and scoring parameters.
Phylogenetic analyses were conducted using the Neighbour-Joining method with the pairwise deletion option for handling alignment gaps and the Poisson correction model for distance computation.
Phylogenetic and molecular evolutionary analyses were conducted using the neighbor-joining (NJ) method [ 30] implemented in MEGA, with the pair-wise deletion option for handling alignment gaps, and the Poisson correction model for computing distance.
All assemblies were processed using CLC Genomics Workbench version 4.8 (CLC Bio) with an option for global alignment that requires exact matches of the 5′- and 3′-end sequences during assembly.
The genomic alignments against the P. aeruginosa reference genomes were done with the MUMmeralignment suite [ 54] using the maxmatch option for nucleotide alignments.
The programs were run using the default options for protein alignment, except for Mafft and Muscle.
Although we used standard alignment options for our genomic alignments using TopHat (Trapnell et al., 2009), we observed that the TopHat alignments generally had fewer aligned reads than the transcript alignments used by our PSG methods.
