Hello professional colleagues, please, i have results from DNA Sequencing (16 S) of samples from my anaerobic digesters. The sequencing results have further been run via Qiime pipeline. However, I am not an expert in microbiology or molecular biology. Please, can anyone advise me on how to do the phylogenetic tree, separate the methanogenic archaea, or the different microbial groups, plots, etc. I can view the results in on Qiime 2 view, but that appears to be all I know for now. Any advise will be highly appreciated. Thanks.
In short you could refer the similar studies and try to do the same/similar with your data, follow tutorials and there are a lot of good ones available on the internet. And if you want any detailed and specific answer, that is not possible without looking on the data and careful analysis.
What you have asked is not a straightforward question. Basically you need to cut your dataset for different parts of question, what you explained. What I think, try using 'shiny phyloseq' which is not super difficult. But here you can start learning how can you do it. Indeed it would take sometime before you get something...
For making phylogeny tree, Blast your sequence in NCBI Database. Based on similarity, make phylogenetic tree using MEGA 7 Software.
You can use pipelines like http://ebg.ucalgary.ca/metaamp/ , that generates your community data in text file formats, which you can further simplify using excel.
Sebastian Euler
It used to be a suitable database however in present times, Greengenes is not at all a suitable database and I would not recommend it.
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