Deleting constant site columns OK?

Question

[dieter]

Hello all, I have another beginner question: Is it true, that in an MSA 100% constant positions (columns which only contain the same nucleotide or amino acid in all sequences and no gaps) can be deleted from the alignment without losing any phylogenetic information? Thanks Dieter

[Joe]

I'm no expert on this, but I think it would depend what you intended to do with the MSA. If you were to draw a tree from it, the tree might be correct, but it may affect the ability to bootstrap replicate (since it discards columns at random and redraws based on the new info). Someone who knows better feel free to correct me.

[dieter]

Thank you ymaule and jrj.healey, Yes, I use the MSA for MrBayes and RAxML to compute phylogenetic trees. OK, that helps - I also thought that way but found very different answers. If someone has more information or hints, please let me (and others) know. Thanks Dieter

Answer 1

[fishgolden]

No. Because the columns have information. It'll change branch length of the phylogenetic tree at least.