I am trying to perform phylogeny analysis on an assembled genomes. From BLASTn searchI got 250 genomes. I am looking to generated phylogeny tree using these genomes and the assembled genome. However, all programs I have used till now like, Mugsy, Clustal Omega, Mafft, failed in producing alignment for these genomes. The length of these genomes is about 80,000 bases to 100, 000 bases. Can you please let me know how can I perform phylogeny analysis using these genomes?
I have performed phylogeny analysis at gene level using the terminase subunit of these genomes, and got the results too, but I am interested in performing genome level phylogeny analysis. Thanks!