I have fastq file of 16S next gen sequencing data of gut microbiota. How I can perform phylogenetic and statistical analysis to estimate diversity using software that run on windows?
You can try following link to learn about metagenomic analysis. https://galaxyproject.github.io/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html#shotgun-metagenomics-data
You can use - usegalaxy.org for metagenomics analysis from windows.
Exactly! @Kevalkumar shah is absolutely right. You can try Galaxy, but still for that too, you need to have a bit basics of NGS data analysis and bioinformatics. You can also try Unipro Ugene (google it).