How to draw phylogeny tree of 1100 genomes belonging to diffrent linages of same spices, Where each sequence consists of ~100000 SNPs locations of genome, I tried 'msa' package with default parameters, but it is taking much longer time. Please suggest me any trick to do this.

I do not understand why you use 'msa' for that purpose. If you are considering SNP data, the SNPs are already aligned, so there is no need to align the genomes. I also wonder how you can deal with SNPs across different species. Please specify in much more detail what your setup is and what you want to do.