From Biological Sequences to Multidimensional Scaling
From BIOlogical Sequences to MultiDimensional Scaling
Links elements in a mmds object to specific groups and colors
Difference score
Dissimilarity score
Writes a MSA file in FASTA format
Extraction of clusters alignments
Reads a file in FASTA format
Reads a multiple sequence alignment file in MSF format
Multiple runs of K-means analysis
Matrices of difference scores between sequences
Matrices of dissimilarity scores between amino acid sequences
Plots the mmds coordinates onto a 2D space
Plots the mmds coordinates onto a 2D space
Display the mmds coordinates onto a 3D space
Plots a summary of the mmds results
Metric multidimensional Scaling Projection
Metric multidimensional scaling
Random Alignment
Plots the eingenvalues of an MDS analysis
Silhouette score
Writes PDB file
Utilities dedicated to the analysis of biological sequences by metric MultiDimensional Scaling with projection of supplementary data. It contains functions for reading multiple sequence alignment files, calculating distance matrices, performing metric multidimensional scaling and visualizing results.