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The NW alignments are performed and a matrix of sequence distances built.
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A matrix of combined sequences was constructed for the 371 individuals examined, and showed that 30 different cpDNA sequences (haplotypes) were present.
A matrix of concatenated sequences was built whenever the COI and ITS1 fragments came from the same individual.
In order to reduce the immunogenic potential of rat αD11 [ 25] in the dog, changes were made to the heavy and light chain variable domain framework sequences by alignment with a matrix of predicted protein sequences encoded by expressed canine IgG cDNA sequences.
From the multiple sequence alignment (MSA) of the active sequences, we computed a matrix of pairwise distances, based on sequence identity.
Peptide sequences with probability score of 95 percent and higher were retained in the dataset and used to generate a binary matrix of sequence-to-microbe assignments.
These sequences were added to a large matrix of sequences from other Ascomycota, which was then analyzed both by maximum parsimony and Bayesian inference.
The results are best visualised as a tabulated matrix of sequencing barcode versus spike-in barcode for each library (e.g., full results in Additional file 7: Table S6).
In the final exercise, students constructed a relatively large and complex tree from a matrix of 25 hypothetical DNA sequence positions for 13 taxa.
Let be a matrix of real numbers and a sequence of real numbers.
With this initial search, we obtained a matrix of 63824 scores (3989 protein sequences blasted against 16 genomes) providing two types of output: categorical (hit versus no hit) and quantitative (degree of similarity).
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