Entering edit mode
4.5 years ago
marina.gerges
•
0
Hi guys, I am trying to get a heatmap for Multiple sequence alignment using a matplotlip module in Python, and on the right side i want to have a phylogenetic tree. For the MSA, I used Muscle. I tried to google but couldn't really understand how this can work. Can someone help? Thank you
Please provide more information. Its not clear what a 'heatmap for an MSA' exactly is?
Creating the type of figure you want to create in matplotlib may be quite tricky.
I mean, I want to use alignment scores from MSA, then use it to get a heatmap. And I think for that i need to cluster first may be by seaborn. but I don't know, It is really tricky at least for me.
What do you expect to visualize in a heatmap from a multiple sequence alignment?
I thought I can use the alignment scores as an indication for % identity to cluster and then get a heatmap.
Alignment scores are not the same as
%ID, so you'll need to decide which of these measures you want to use.If you want a heatmap showing the similarity between all sequences vs all other sequences, then you really want to do multiple pairwise alignment rather than true multiple sequence alignment. You can put that heatmap in to various R and python packages to perform simple hierarchical clustering of the actual scores if thats what you want.