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 3), 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!
Firstly, its 2017, start using MEGA7.
Secondly yes I've had that problem. You need use a the button (Diagonal arrow) which will allow you to adjust dimensions of the tree.
However, this isn't always great. You may need use something like FigTree.
You've got a lot of sequences in your data set so it can be difficult to align it in a nice manner. You can always see if you can export the tree in a different file format and open it in an R package.
Try MEGA7, it has several improvements. Also, test FigTree.
If your objective is clear, MEGA will give you good results. Distance is shown in 1st figure, but when you take consensus, distance cant be computed as consensus as it is only for Bootstrap values.
The problem is that you try to add scale bars to a bootstrap tree. The answer is here
http://www.megasoftware.net/webhelp/faqs_rh/why_can_t_i_display_branch_lengths_for_a_bootstrap_consensus_tree_.htm
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