Sentence examples for multiple alignment mode from inspiring English sources

NCBI accession numbers for all sequences used in the phylogenetic analysis are listed either in Figure  3 or in Additional file 3. The sequences were aligned using the ClustalW (version 2.0.12) program [ 80] in the multiple alignment mode and the neighbour-joining unrooted tree was generated with PHYLIP 3.67 [ 81].

DNA sequences of AVD, AVR2, AVR4, AVR6, AVR-A, AVR-B, AVR-C and BBP-A and BBP-B were aligned exon by exon and intron by intron using Clustal X in multiple alignment mode with default values for both pairwise and multiple alignment parameters.

For comparison of the primary structures of biomineralization proteins and their families and groups, the multiple sequence alignment mode "Align" was used, implemented through "ClustalW 2.0.12" (with the mode settings not configured).

Phylogenetic trees were built using the online service phylogeny.fr [35] ("Advanced" Mode, no multiple alignment, all else default) which implements PhyML [36] for the construction of phylogenetic trees and treedyn [37] for producing the images presented here.

Perfect matches to the reference genome and transgene constructs (if applicable) were identified using bowtie in -v alignment mode, allowing for multiple matches (Langmead et al., 2009 ).

The input alignments (SWISS-MODEL "alignment mode") were based on a structural multiple alignment calculated by 3DCoffee which was manually refined to result in optimal pair wise target-template alignments (to be modeled SOB/SRB AprBA versus the A. fulgidus sequence).

The aligner was run in end-to-end alignment mode.

A phylogenetic tree is then created from this multiple alignment using PHYLIP [ 27], which has been modified to run in batch mode, to build rooted and unrooted trees.

23 Psiblast was used for the Multiple Sequence Alignment (MSA) generation method with three MSA generation iterations and a local alignment mode.

The multiple alignment of the full length amino acid sequences was generated using M.A.F.F.T. v6.717b [ 32] in the 'auto' mode and was subsequently manually curated (removing regions of poor alignment quality) using Jalview v2.7 [ 73], resulting in 501 columns that were used for phylogenetic inference.

multiple alignment using fast Fourier transform.