# From Biological Sequences to Multidimensional Scaling

## Documentation for package ‘bios2mds’ version 1.2.3

- DESCRIPTION file.

## Help Pages

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