Thanks for posing the question. Our website is designed for efficient statistical analysis of microbiome data. The filter step is necessary for getting meaningful statistical result in most cases and also computational friendly. If you want all the features to be processed, you can run the analysis locally using R packages such as phyloseq. Our new package MicrobiomeAnalystR will be released soon, which will also be a good choice.
If you have more consideration or suggestion, feel free to contact us.