Try:

boot.phylo(nj(dist),dist,FUN = function(xx) nj(xx),B=100)

dist contains your distance matrix

I am using R, with the package ape. I use distance according to Jacquard. and not Neighbourth joining....

You can calculate the distance using Jaccard (or any other distance measure) and use Neighbourth joining (or other distance based phylogenetic methods) to calculate the tree. Just try the aforementioned approach using your own dist object as calculated in your port.

the mentioned formula gave:

boot.phylo(nj(dist),dist,FUN = function(xx) nj(xx),B=100)

| | 0%Erreur dans x[, boot.samp] : nombre de dimensions incorrect

(error; number of dimention incorect)

other idea?

I have a data set in excel exported from presence and absence of bands in an AFLP analysis (dominant markers). I have done alot of work with R but I am trying to make a phylogeny using R, which I am confused in formatting this data for dendogram. Is there any body to give me an example of correct format for this data set and also related script and package I need in R for analyzing and plotting phlogeny tree.

@Majeed Askar... you can construct dendrogram with number of R packages. However, i use pvclust package (the most recent). This package offers simultaneous bootstrapping by using multiscale resampling. In addition, the dendrogram generated provides approximate unbiased p-value which is a more reliable than bootstrap probability p-value.

Unlike other way of construction of dendrogram using data matrix - the variables should arranged in column.

Script:

> # draw dendogram with red borders around the 5 clusters

> library(pvclust)

> fit plot(fit) # dendogram with p values

> # add rectangles around groups highly supported by the data

> pvrect(fit, alpha=.95)

> result10k

I am working with a polyploid SSR dataset. I have successfully made a distance matrix using the package "polysat":

testmat

I have made my tree like this...but unable to add node values...please give me the commands...here is what I have done in rstudio in simple way from clustal alignment...

> setwd("C:/Users/lenovo/Desktop/Partha project")

> getwd()

[1] "C:/Users/lenovo/Desktop/Partha project"

> x=read.phyDat("ansu.clustal", format="clustal")

> dm treeUPGMA plot(treeUPGMA, main="UPGMA") 

Hi @Parthasarathi Tripathy… are U trying to add the value or to compute them? 

Dear SM Reddy,

I am not sure with your kind of SNP data as I have not worked on it. I suggest you to refer this site http://www.sigmath.es.osaka-u.ac.jp  for more information