r - How to select a genetic distance range to plot a mst using vengan library -

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i've tried perform genetic distance analysis using ape , vegan. first of calculated genetic distances using ape:

data<-read.dna(file = "proof.txt", format = 'fasta') d <- dist.dna(data, model ='tn93', as.matrix ='true')

this code gives me huge matrix d = 0 in many cases. then, perform mst follows:

mst <-spantree(distances, toolong = 0.015)

i chose toolong select max parwise distances = 0.015

but when i've tried plot it, error apeared:

error in fun 8d, y):zero or negative distances between objects 1 , 2

does know how choose distances larger "0" , >= 0.015?

supply configuration on plot spanning tree.

the error message comes function mass::sammon() used find configuration of points if none given, , function not accept 0 distances. instance, following should work:

plot(mst, ord = cmdscale(as.dist(dist.dna)))

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