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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.

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  • $\begingroup$ What format is your alignment file in? Have you considered NCBI MSA Viewer or the Genome Workbench $\endgroup$ – vkkodali May 23 at 10:27
  • $\begingroup$ It is in fasta format and the file size is 27 MB (too big for NCBI MSA viewer). $\endgroup$ – Shilpa Janarthanan May 23 at 13:11
  • $\begingroup$ How about using Genome Workbench then? It probably does not have size limits. $\endgroup$ – vkkodali May 23 at 16:10
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Try to use the MEGA software. You download in this website: https://www.megasoftware.net/

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  • $\begingroup$ We're looking for long answers that provide some explanation and context. Don't just give a one-line answer; explain why your answer is right, ideally with citations. Answers that don't include explanations may be removed. $\endgroup$ – WYSIWYG May 23 at 11:42

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