Hello all, I am currently trying to construct a phylogenetic trees for a large number of bacterial assemblies (hundreds to thousands) derived from the same bacterial species. I am quite willing to lose a lot of the data and to use only the 16S sequences or a small subset of genes. Unfortunately, it seems many phylogenetic and phylogenomic methods are not capable of handling such a large number of sequences. Does anyone possibly know of a method that might be able to construct the tree I am looking for? We have a large cluster available and can spare up to several weeks for the construction.
Many thanks, Yair