Question: Deleting constant site columns OK?
0
gravatar for dieter
17 months ago by
dieter0
dieter0 wrote:

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

homology alignment phylogeny • 565 views
ADD COMMENTlink modified 17 months ago • written 17 months ago by dieter0

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.

ADD REPLYlink written 17 months ago by jrj.healey12k

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

ADD REPLYlink written 17 months ago by dieter0
2
gravatar for fishgolden
17 months ago by
fishgolden390
fishgolden390 wrote:

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

ADD COMMENTlink modified 17 months ago • written 17 months ago by fishgolden390
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1955 users visited in the last hour