" Compute a distance matrix

*simqual o=fish2.nts c=j r=outj.nts d=col

" Do a cluster analysis of the distance matrix

*sahn o=outj.nts r=outjupgmatr.nts cm=upgma

*sahn o=outj.nts r=outjsingletr.nts cm=single

*sahn o=outj.nts r=outjcompletetr.nts cm=complete

" Compute cophenetic values

*coph o=outjupgmatr.nts r=outjupgmacoph.nts

" Compute the cophenetic correlation

*mxcomp x=outjupgmacoph.nts y=outj.nts

" Display phenogram

*tree o=outjupgmatr.nts

" do a consensus tree of single and complete trees

*consens o1=outjsingletr.nts o2=outjcompletetr.nts r=jconssincom.nts

" Display phenogram

*tree o=jconssincom.nts

" Use PCOORDA to obtain an initial configuration

*DCENTER O=outj.nts R=distCentered1j.nts

*EIGEN O=distCentered1j.nts N=3 R=init1j.nts

" non-metric MDSCALE using initial solution

*MDSCALE O=outj.nts N=3 I=init1j.nts R=final1j.nts D=col SC=stress1

" rotate result for ease in viewing

*SIMINT O=final1j.nts C=varcov R=vcv1j.nts D=row

*EIGEN O=vcv1j.nts N=3 R=vect1j.nts

*PROJ O=final1j.nts D=col F=vect1j.nts R=FinalRotated1j.nts

*OUTPUT O=FinalRotated1j.nts

" plot the final rotated configuration

*MXPLOT D=row O=FinalRotated1j.nts G=jmst.nts

"*MOD3D O=FinalRotated1j.nts G=jmst.nts

" computer distance for output from mdscale

*SIMINT O=final1j.nts C=euclid R=euclidj.nts D=col

" use mxcomp to get the coph. corr

*MXCOMP X=euclidj.nts Y=outj.nts