bios2mds-package        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
