I would like to establish an identity cutoff to define a cluster/genotype (it's about a RNA virus).
Dear Renata. One of my friends talk to me about the Arlequin software in order to establish the identity cutoff (an analysis called Pairwise Sequence Comparison, or just PASC) but this software is very tricky (my personal opinion) for that reason I use the R package, through the use of the PEGAS module, specifically the MMD function (Mismatch distribution).
Dear Renata,
You can see the phylogenetic tree and % of identity between one or more sequences with software Geneious.
http://www.geneious.com/
I'm using Geneious, but since it's a lot of sequences I would like a software to help me to do a graphic and visualize it better, to stablish a cutoof like it was made in the paper attached. I think that the R package should do that, I'm trying to figure it out how ;) thank you, guys (sorry for my English mistakes)
The NCBI PASC (pairwise sequence comparison) tool was made for this problem: http://www.ncbi.nlm.nih.gov/pubmed/23012628
http://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi?textpage=overview
But you should also consider the phylogenetic tree, and other factors such as the host range of each virus.
Geneious is too expensive but want to have that software...how can i download the full version?
Hi, Orlando, I did the PASC analysis, it was very helpfull! thank you!
- Badges
- Science method
- Similar topics
- Biological Science
- Evolutionary Biology
- Phylogenetics
- Phylogenetic Analysis