Dendogram construction

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Martin Boys

Nov 6, 2022, 11:45:02 AM11/6/22
Dear Kamvar

Is there any possible way for me to bypass this error which I encountered when trying to plot a dendrogram. My dataset consists of 55 individuals, 10 loci, 3 populations and 1 stratum. Kindly see below the scripts and the outputs in bold which have led to the eventual error. Thank you in advance for your time and assistance.  






This is a genclone object


Genotype information:


    4 original multilocus genotypes

   55 haploid individuals

   10 codominant loci


Population information:


    1 stratum - Pop

    3 populations defined - Hybrid, Heirloom, Grape







> = 0.5)

>NJT1 <- last_plot()

###Bootstrap loci###


>aboot(mic10, dist = provesti.dist, sample = 55, tree = "nj", cutoff = 50, quiet = TRUE)

Phylogenetic tree with 20 tips and 18 internal nodes.

Tip labels:

  T-69, T-77, T-2, T-63, T-46, T-58, ...

Node labels:

  NA, NA, NA, NA, NA, NA, ...

Unrooted; includes branch lengths.

Warning message:

In aboot(mic10, dist = provesti.dist, sample = 55, tree = "nj",  :

Some branch lengths of the tree are negative. Normalizing branches according to Kuhner and Felsenstein (1994)


Error: Number of rows in data frame not equal to number of individuals in object.

Zhian Kamvar

Nov 7, 2022, 3:01:24 PM11/7/22
to Martin Boys,
Hi Martin,

Before you post, check carefully the lines of code you are submitting. When you make an assignment, try printing the output and ask yourself "does this give me what I think it is giving me?
You are trying to set the strata from data.frame(other(martin25)). What is in `other(martin25)`? Likely, there is nothing there.
Read and see if that clears up the question about strata.


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