Sentence examples for multiple alignment using from inspiring English sources

These clusters were aligned by Multiple Alignment using Fast Fourier Transform MAFFTT) (Katoh et al. 2002) and concatenated, followed by tree construction using PhyML (Guindon et al. 2010).

Protein sequences of BVMOs (Additional file 1: Table S1) were aligned with MAFFT (Multiple Alignment using Fast Fourier Transform) version 7 (Katoh and Standley 2013).

Sequences were aligned with MAFFT (multiple alignment using fast Fourier transformation, v6.832b) using the "G-INS-I" parameters [ 28].

The new sequences (31) were re-aligned to the original multiple alignment using T-coffee.

Sequences were aligned using the MAFFT (Multiple Alignment using Fast Fourier Transform) web server at the European Bioinformatics Institute [ 57].

The phylogenetically nearest top-hit full-length sequence was designated as the reference sequence onto which all toxin family-specific reads were aligned to create a multiple alignment using COBALT [ 99].

Each PCG was aligned individually with codon-based multiple alignments using MAFFT as implemented in the TranslatorX online server [ 56].

We generated multiple alignments using PRANK31 [ 56] and eliminated poorly aligned sites using Gblocks [ 57] before performing a standard McDonald-Kreitman test [ 22].

MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.

Subsequently, conserved elements were predicted in the multiple alignments using PhastCons with the following inputs and parameters: the neutral and conserved models, target coverage of input alignments = 0.3 and average length of conserved sequence = 45 bp.

The sequences were assembled and then subjected to multiple alignments using DNAMAN ver. 6.0 (Lynnon Biosoft) and consequently MAGA ver. 6.0 (Tamura et al. 2013).