Pair wise evolutionary distance tree

Question

[shameera.dev]

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!

[Joe]

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.

[shameera.dev]

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?

[Joe]

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.