Hi biostars! I know that substitution matrices are used to reconstruct evolutionary trees. My question is what roll do they play in the reconstruction (how does it work)? and what are the results in the reconstruction if you use a different matrix? you get another tree?
thanks for the reply!
•
written
by
loicatraile •
1 answer
Substitution matrices are used to quantify the 'difference' between amino acids or nucleotides between species. For example BLOSUM. For biochemical reasons, a change from His to Glu is not as 'bad' as a change from Glu to Cys. Based on these scores you can then calculate a phylogenetic distance between species. So to answer your questions, the substitution matrix may change your tree depending on your data. Generally however, these changes are details, which may or may not be important.
Log in to answer this question.
-
Jensen-Shannon Divergence (Capra and Singh, 2007) scored with substitution matrix for conservation …
written by Jonathan Lefebre •
-
Algorithm for initial tree topology for Parsimony tree
written by mdsiddra •
-
what standard deviation mean according to distance matrix??
written by eng_samar_zayed •
-
Basic question about protein distance with multiple sequence alignment
written by bds1217 •
-
Choosing phylogenetic approaches
written by Yongjie Zhang
-
Species tree vs Gene trees during evolutionary analyses: Does it matter?
written by ishengomae
-
Multi-Sample Vcf To Phylogenetic Tree.
written by William
-
Where Is Pam 1.0.7 Source (To Generate Pam Substitution Matrices)?
written by The Original Gtk
-
What Substitution Matrices Are Available For Blast?
written by Ryan Thompson
-
Phylip Distance Matrix Question
written by Deena •
