From Biological Sequences to Multidimensional Scaling

Documentation for package ‘bios2mds’ version 1.2.3

bios2mds-package	From BIOlogical Sequences to MultiDimensional Scaling
bios2mds	From BIOlogical Sequences to MultiDimensional Scaling
col.group	Links elements in a mmds object to specific groups and colors
dif	Difference score
dis	Dissimilarity score
export.fasta	Writes a MSA file in FASTA format
extract.cluster	Extraction of clusters alignments
gpcr	Pre-analyzed G-Protein-Coupled Receptor (GPCR) data set
import.fasta	Reads a file in FASTA format
import.msf	Reads a multiple sequence alignment file in MSF format
kmeans.run	Multiple runs of K-means analysis
mat.dif	Matrices of difference scores between sequences
mat.dis	Matrices of dissimilarity scores between amino acid sequences
mmds	Metric multidimensional scaling
mmds.2D.multi	Plots the mmds coordinates onto a 2D space
mmds.2D.plot	Plots the mmds coordinates onto a 2D space
mmds.3D.plot	Display the mmds coordinates onto a 3D space
mmds.plot	Plots a summary of the mmds results
mmds.project	Metric multidimensional Scaling Projection
random.msa	Random Alignment
scree.plot	Plots the eingenvalues of an MDS analysis
sil.score	Silhouette score
sub.mat	Amino acid substitution matrices
write.mmds.pdb	Writes PDB file