Hi, I am new to Bioinformatics! :)
What I am looking for is a tool or software that once the Phylogenetic Tree is created( whichever method used) that I can select one sequence on the tree and compare it to other sequences of my choosing, and it will show all the similar mutations of X length and highlight it in the genome or highlight the data where I can visually see all the areas of these similar blocks of mutations. Perhaps a graph of findings.Also, sequences that have these mutations similiar in a specific partition but are different in the rest.
For example, how many nucleotides of length 3-5 are in the same in the sequence X, Y, Z species that I choose but are not in Species A,B.
A friend mentioned a Tolerance Tool was being used in one software was it was very tedious
I hope I am making sense. Any guidance would be greatly appreciated. Thank you
Victoria
I very much doubt you're going to find one tool that can do all of what you're asking.
If you want to look for mutations etc between sequences, that's largely a task that BLAST can probably help with. Their taxonomy browser can identify other species which contain your sequence of interest.
Otherwise, Jalview, Mesquite and MEGAN are probably the most fully featured interactive alignment/tree browsers I can think of
Seems like they would a tool that could compare sequences from different nodes within and single tree, saying where they are similar and where they are different
What exactly is it you are trying to show? Where the sequences differ isn’t super useful information on its own.
Perhaps if you explain the goal more there might be an alternative approach that could work.
Yes your right, I need to find a way to explain exactly what I need.
A tool that takes one sequence of the tree and compares against the other sequences that are not in the same node.
Showing areas of mutations that are same from strains of virus that are on different branches.
Maybe like a partition tool.
lol, sorry I am not sure that even sounds better.
let me try to think of a different way .
Please don’t add answers, these are all comments. I’ve moved it for now.
All of this information is in the multiple sequence alignment your tree is created from.
Would it help to order the sequences by the order within the tree so they can be looked at?
Which software can I use that will allow me to look at the similarities and differences between multiple sequences.
I think I need to some more time reading about the softwares being used. Which software do you recommend.
Thank you for helping me.
find conserved mutations within the genome between species that make graph or a plot