Softwares

1. R:
• Package: stats
• cmdscale(): classical (metric) MDS (an example can be found here)
  


• Package: proxy
• dist(): distance matrix


• Package: MASS (Mondern Applied Statistics in S)
• isoMDS(): Kruskal's non-metric MDS (an example can be found here)
• Shepard(): for drawing Shepard diagram
  
• sammon(): Sammon's non-metric MDS (similar to Kruskal's non-metric MDS but independently developed)
  


• Package: smacof (Scaling by MAjorizing a COplicated Function; a paper is here)
• smacofSym(): for symmetric dissimilarity matrices
• smacofRect(): for rectangular input matrices, i.e., unfolding
  
• smacofIndDiff(): individual difference MDS
• smacofSphere.primal(): projection of the resulting congurations onto spheres
• smacofSphere.dual(): indirect function to solve linear problems, sometimes faster than primal
• sim2diss(): convert similarity matrix to dissimilarity matrix
  


• Package: labdsv (Laboratory for Dynamic Synthetic Vegephenonenology)
  
• nmds(): application of isoMDS()


• Package: vegan (R functions for vegetation ecologists)
  
• metaMDS(): an integration of initMDS(), isoMDS(), postMDS(), and wascores()
• procrustes(): for the Procrustes Problem
• wcmdscale(): weighted classical (metric) multidimensional scaling
  


• Package: rggobi
• ggobi(): interactive multidimensional scaling using ggobi and ggvis for display
  


• Useful Links
• Task View of the Comprehensive R Archive Network
• Notes on the use of R for psychology experiments and questionnaires: here via here
  
• R site search
  


2. SYSTAT:
• use EM to estimate missing data in nonmetric unfolding model
• power transformation (metric MDS)
• log transformation (metric MDS)


3. PERMAP: a highly entertaining, interactive tool to explore perceptual mapping
   


4. SPSS: proxscal, prefscal, alscal


5. MATLAB: mdscale()

A more complete list of MDS softwares can be found here.