ambiguities in an alignment

[Francisco J. Ruiz-Ruano Campaña]

Dear Phyloviz staff,

I run Phyloviz online in an alignment with ambiguities, i.e., “R” for purines (“A” or “G“), for examples. Did Phyloviz consider ambiguities or, alternatively, removes positions and/or sequences with ambiguities?

Thanks in advances,

Francisco.

[ramirma]

Dear Francisco,

We apologize for the long absence of a response. PHYLOViZ will consider that a different position if it is an A or a G in another sequence, but as identical if it is an R. It will still consider all the positions in the alignment. It will not however, use any distance matrix or table to take into account that this position could be in fact be 0.5 identical to an A. I hope I was clear in my response.

Thank you for using PHYLOViZ