Sentence examples for alignment were conducted from inspiring English sources
Phylogenetic analyses of the amino acid alignment were conducted with MrBayes and PhyML 2.4.5 [ 37].
Additional rounds of alignment were conducted with successively lower levels of sequence similarity.
Quality ascertainment and sequence alignment were conducted in SEQMAN™ version 6.1.
Sequence quality assessment and alignment were conducted with CLC Genomics Workbench (version 5.0; CLC bio, Cambridge, MA, USA).
Phylogenetic analyses of the alignment were conducted using Protpar on the Phylip package [ 33] through the PIE Phylogeny Interface Environmentt) suit at.
Briefly, after transforming the raw Agilent data into MZ-mine format, automatic integration and peak alignment were conducted for subsequent explorative data analysis.
A multiple genome alignment was conducted by aligning contigs from the different assemblies to the PacBio reference assembly to identify conserved regions and to evaluate gaps in the different DSM 10061 assemblies.
After manual inspection and editing where necessary, sequences were aligned using ClustalX [33]; the intron alignment was conducted by taking into account secondary structure following Goddard and Burt [6].
Sequence alignment was conducted with BLAST tools provided by the National Center for Biotechnology Information.
Alignment was conducted using ClustalW within MEGA6 (Tamura et al. 2013), gap opening penalty 5; gap extension penalty 1.5 was set for both pairwise and multiple alignments.
Sequence alignment was conducted using ClustalW, and a maximum-likelihood tree with 100 bootstrap replicates was constructed using MEGA version 4.0 (Tamura et al., 2007).
