Sentence examples for alignment to visualize from inspiring English sources

A neighbor-net analysis was then performed on the full plastome alignment to visualize character state conflict using the SplitsTree4 v. 4.13.1 [ 58].

As a first step, we performed a multiple alignment of all the zinc finger regions of the C2H2-ZNF genes of interest; we removed all the sequences that were not unambiguously alignable and generated a new alignment allowing to visualize sequence similarity between the finger motifs of the various genes.

The BLAST tool [ 162], CAP3 assembler [ 163], ClustalW [ 164], and Treeview software [ 165] were used to compare, assemble, and align sequences and to visualize alignments.

These genome alignments also served to visualize and quantify the overall quality of the individual draft assemblies for the test strains.

Alignments were edited with the JalView [59] editor which allows the user to visualize alignment conservation via various residue coloring schemes as well as conservation and consensus plots.

The ability to visualize alignment of sequencing reads mapped against a reference also allows identification of structural variation.

These features of JBrowse enables the users to upload BAM files as tracks to visualize alignment files faster as compared to the CGI-based genome browsers and provides pictorial representation for the presence of variations.

The NUCmer function of MUMmer package was used to align scaffolds, and the MUMmerplot function was used to visualize the alignment as a dot plot.

The Genedoc package [85](http://www.psc.edu/biomed/genedoc/) was used to visualize alignments and calculate percent identity of nucleotide and peptide sequences.

JalView was used to visualize alignments [ 73].

In order to visualize alignments, we implemented different chart types.