Hello R users,
Can any one please help me to find a way to build phylogenetic tree by R
program from any distance matrix.
Suppose I have a data like :
MATRIX
[1] '1' 0.0
[2] '2' 0.071 0.0
[3] '3' 0.036 0.286 0.0
[4] '4' 0.429 0.75 0.714 0.0
[5] '5' 0.679 0.179 0.214 0.536 0.0
[6] '6' 0.893 0.929 0.964 0.464 0.357 0.0
[7] '7' 0.643 0.571 0.5 0.607 0.821 0.786 0.0
[8] '8' 0.857 0.393 0.107 0.321 0.25 0.0 0.143 0.0
Or as a vector I have the lower triangle like:
> dist.mat
[1] 0.071 0.036 0.286 0.429 0.750 0.714 0.679 0.179 0.214 0.536 0.893 0.929
0.964 0.464 0.357 0.643 0.571 0.500 0.607 0.821 0.786 0.857 0.393 0.107
0.321 0.250 0.000 0.143
It will be really helpful if anyone can help me to get a tree (between these
8 species) from this vector values. The matrix above I created by hand to
use as a nexus distance matrix data for other methods. So it is better if I
can use this distance matrix vector (dist.mat) directly.
I couldn't find any package for phylogenetic tree from distance any distance
matrix in R.
Thank you very much.
With best regard,
Suparna
----------------------------
[[alternative HTML version deleted]]
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
