Man pages for bios2mds
From Biological Sequences to Multidimensional Scaling
| 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 |
