Hi, everyone.
I've been trying to generate a bacterial 16S rRNA phylogenetic tree with a scale bar. I selected NJ, 1000 bootstrap, and I got original tree and bootstrap concensus tree.
By clicking at each pf them, I found they're lousily crammed but at least had scale bars (attachment 1). Hoping to spread the branch better, I tried "display only topology ", the shape and appearance was what I would like it to be, but there's no scale (attachment 2).
Had "display only topology" button selected, I also clicked "compute linearized tree", nothing actually changed, still no scales, all the species label aligned vertically (attachment 4), I don't know what happened and what to do.
I saw others work online, they had the perfect tree using the same software (attachment 4). That's what I hope to generate with Mega, can anyone help me with my problems? Thank you all for your patience!
https://www.researchgate.net/post/Is_anyone_familiar_with_using_Bootstrap_Consensus_Tree_in_MEGA_software
Has a good discussion of this..
https://www.researchgate.net/post/Is_anyone_familiar_with_using_Bootstrap_Consensus_Tree_in_MEGA_software
I think first of all, you have to decide what kind of tree you want. Does it the best tree of your method? Does it the bootstrap consensus tree, strict or by majority rule? Cladograms or only topology trees are just graphical representations of your tree arrangement they don't reflect the distance of your method. Take a look at the example you showed from the literature. The tree's branches are not linearized because they have phylogenetic distance information, probably that tree is not an only topology either a consensus tree.
Also, I recommend you to export your trees as neweek and load in figtree program. You'll be able to do more graphically on this software.
I hope it helps you.
Good luck.
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