In my case, I need the ready made 16S rRNA Multiple Sequence Alignment File for E.coli and use it to generate the phylogenetic tree file in Newick format. I've tried using the one from utexas website, but I get too many errors when using the alignment file for tree generation, either the file size is too big or the input file is not a fasta file, so I tried to read the alignment file in R using read.alignment() function and it reads fine. Still I get this error when I used it to generate the tree.
So, can someone tell me where do I get a ready made Multiple Sequence Alignment File for 16S rRNA of E.coli being the reference sequence?
Thank you.