Hi, I may have stumbled upon an error in the branch length calculation of the ctc package's hc2Newick function, which converts an hclust object to Newick format. However I am not confident yet to report it as a bug and hence this email to see if you agree with my interpretations below. > hc = hclust(d = as.dist(matrix(c(0, 2, 4, 4, 2, 0, 4, 4, 4, 4, 0, 2, 4, 4, 2, 0), 4, 4, dimnames = list(LETTERS[1:4], LETTERS[1:4])))) > hc2Newick(hc) [1] "((A:1,B:1):0,(C:1,D:1):0);" Shouldn't the correct output be [1] "((A:1,B:1):1,(C:1,D:1):1);" so that the branch lengths and hclust heights agree?? Some more information on hclust heights (easiest to view via plot(hc)): > hc$labels [1] "A" "B" "C" "D" > hc$height [1] 2 2 4 > hc$merge [,1] [,2] [1,] -1 -2 [2,] -3 -4 [3,] 1 2 If my interpretations are correct, then the hc2Newick() function code can be fixed by removing all "dist" calculation statements and putting a single "dist" calculation statement like so: j <- hc$merge[i, 1] #original code k <- hc$merge[i, 2] #original code + dist <- hc$height[i] - (ifelse(j < 0, 0, hc$height[j]) + ifelse(k < 0, 0, hc$height[k]))/2 #new line I'm using R 2.15 and packages: "[1] ctc_1.32.0 amap_0.8-7 Biobase_2.18.0 BiocGenerics_0.4.0". Thanks, Mani PS: Apologies if this email was posted twice, as I wasn't sure if I posted correctly the first time I tried.