Sentence examples for multiple alignments using from inspiring English sources

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].

Multiple alignments using MUSCLE [ 50] were then parsed to remove those poorly aligned regions using the Gblocks algorithm [ 51] with the following criteria: maximum number of contiguous non-conserved positions = 10 and minimum length of a block = 5.

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).

Dendrogram trees were generated from ClustalW multiple alignments, using the maximum likelihood method in the PHYLIP package [126].

As a consequence, iterative algorithms were developed to construct more reliable multiple alignments, using for example iterative refinement strategies [17], Hidden Markov Models [18] or Genetic Algorithms [19].

The final multiple alignments used for the analyses are available in additional file 3.

The final multiple alignments used for the analyses are available from the authors upon request.

This tree and the multiple alignments used to build it were downloaded from iTOL (Letunic and Bork, 2007, 2011).

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).