Alignments

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Visualize your highly customizable alignments with the Alignment View.

Highly Customizable Alignments

Sequence alignments are a powerful way to test sequences for functional, structural, or evolutionary similarity. BioTuple offers both pairwise and multiple sequence alignments for DNA, RNA, and protein sequences. In addition, the user has the ability to choose affine scoring, substitution matrices, and manually entered scores. After completing an alignment the user can visualize the results as compared to a consensus, phylogenetic tree, or statistical data.

Pairwise or Multiple Alignments

BioTuple offers Needleman-Wunsch(global) and Smith-Waterman(local) alignments for pairwise and a progressive alignment for multiple sequence alignments.

Modify Alignment Parameters

BioTuple allows the user to customize the parameters for which an alignment will run. Nucleotide and proteins have independent settings for score values, affine scoring, substitution matrices, and more.

Phylogenetic Trees

Create a visual representation of the relationships between aligned sequences in the form of a phylogenetic tree. View weighted or unweighted trees with distance values constructed with the neighbor joining algorithm.

Consensus Comparison

View a monomer by monomer comparison of each sequence as compared to a consensus determined by the “majority rules” scheme.

Statistical Analysis

View the results of an alignment in terms of numbers as similarity or identity matrices.

Substitution Matrices

Choose between several common substation matrices including BLOSUM, PAM, and DNAFull.