Constructing A Nj Tree From A Binary Matrix With 11 Taxa And 370.000 Characters.

Question

[Biojl]

Hi,

I want to construct a NJ tree using a matrix containing about 370.000 rows that would be the characters, they can either be 0 or 1 and I have 11 taxa or columns.

Could you recommend me a free-software that could handle this tree-construction in a regular workstation (8 cores, 60gb RAM).

I've been looking at Mesquite, any experiences with it? What is the character 'limit' for a nexus file, is it fixed by some softwares?

Thanks!

Answer 1

[Zev.Kronenberg]

How about using the Ape package in [R]?

[Biojl]

Thanks! The computational time was almost 0. I also used the Dist function inside the 'amap' R package to build the distance matrix in case anyone is interested.

Answer 2

[Josh Herr]

As far as Mesquite is concerned, I think it's a great program. Here's a good tutorial. I haven't approached a character limit for nexus files, so I am not sure if one exists. The program Mesquite morphed out of the similar MacClade and there were limits to the size of nexus files in MacClade.