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4.2 years ago
shameera.dev
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Hi... Im Devinda, a beginner for bioinformatics, I would be so thankful if someone could explain how I can prepare a phylogenetic tree based on pairwise evolutionary distances. All I have is a bunch of viral sequences and have no idea where to begin with.... Thanks!
I wouldn't use pairwise differences.
Generate a multiple sequence alignment of your sequences using one of many tools (
muscle
,clustal
,MAFFT
etc).Then generate a tree using a dedicated tool such as
IQTREE
.Thanks Joe, What I really want to do is to figure out whether a novel sequence is really novel or just a variant of existing viruses. I heard that pairwise evolutionary distance tree could solve it! Is there any other tool to do my job?
What do you mean by novel? Never seen before?
Everything is a variant of something that already exists - that's evolution.
I would start with multiple sequence alignment anyway, as I'm not sure exactly why you'd have heard that about pairwise (but I might be wrong). If your sequence is that novel, it will probably be an outgrouping relative to the other sequences in the dataset.