Create phylogenetic tree visualization from handful of 16SrRNA .fastq sequences

Question

[suzuBell]

I have the 16S rRNA sequence of a new strain of bacteria. I would like to make a simple phylogenetic tree visualization comparing this new strain of bacteria with about 12 other strains of known bacteria. Currently, I have 13 .fastq files (one being the new strain of bacteria), each containing a 16S rRNA sequence.

1) What is a simple pipeline for creating a phylogenetic visualization based on these 16S rRNA sequences (currently in .fastq format)? This is similar to a previous question I asked, but I remain unclear on how to then construct the phylogenetic visualization. Are there any pipelines that make the alignment, tree construction, and visualization process more streamlined?

2) Is my approach here suitable? I hand-selected 12 species that are supposedly similar to this new strain (based on the scientists who gave me the data). Is it common to construct bacterial phylogeny tree based on 16S rRNA (instead of, say, 23S rRNA or a protein-coding gene list, which seems more time-consuming)?

Answer 1

[Mensur Dlakic]

Lots of programs for various aspects of molecular phylogeny can be found here.

After gathering your 16S rRNA sequences, a step-by-step pipeline would look something like this:

1) align the sequences (I recommend SSU-align, but many people use MUSCLE or other regular alignment programs)
2) trim the sequences (I use trimAl, but there are other options)
3) run tree reconstructions (MrBayes, IQ-TREE, RAxML, BEAST, PhyML, PhyloBayes, take your pick)
4) visualize the tree (FigTree, TreeView, MrEnt, PhyloWidget, ETE, Mesquite; I sometimes use MEGA just for visualization)

http://etetoolkit.org/

Here is a video tutorial showing how to do all these steps in MEGA.

I do not recommend MEGA as the best solution for this particular task - far from it, but it includes most of the steps in one package. It should not be too difficult to find MEGA-based tutorials.