I have been going through documentation for Qiime and Metaphlan and am trying to understand the difference between the two. I do understand that Qiime is a full fledged tool that includes all steps from demultiplexing, denoising to statistical analysis and plots. Metaphlan seems to be for identifying the composition (or abundance) of individual microbes in each sample. However I do understand that taxonomy identification is possible in Qiime using a classifier from the q2-feature-classifier plugin, which means it does everything that Metaphlan does ?
To make things confusing for me, there is also a qiime metaphlan plugin (q2-metaphlan2). Is this just another option for identifying taxonomy from qiime instead of the q2-feature-classifier plugin ?
Also on checking metaphlan docs, it allows to use fastq files as input directly, which makes it good enough as a standalone tool.
I do feel that comparing qiime and metaphlan is incorrect and is like apples to oranges, but just can't get a clear idea.
A related question in qiime forum ( https://forum.qiime2.org/t/metaphlan2-vs-vsearch-for-fungal-metagenomic-shotgun-sequences/6536/4 ) does shed some light, but I'm still not quite clear.
Can someone please explain to me which of qiime2 or metaphlan I should be using to perform comparison between different groups or for obtaining relative abundance from 16s data or metagenomic shotgun sequence data ?