Qiyun Zhu

_Originally posted by @gwarmstrong in https://github.com/qiyunzhu/woltka/pull/1_

I carefully thought about this, and figured that there is a good solution: combine `--ranktb` and `--map` into one format. It will be a tab-delimited file with arbitrary number of...

I thought more carefully and planned to do the following: I still want to keep `--map` and `--rank-table` as two parameters. I think they represent two file formats, both of...

Hello @ebolyen would you like to comment on whether the consideration of edge cases (empty community, one-species community) is sane in this PR (see my comments above)? Also cc'ing @gregcaporaso

Now there is a significant enrichment of the parameters and documentation of alpha diversity metrics.

@wasade @mortonjt Here is a very large PR. I did some substantial amount of literature review in order to improve the calculation and documentation of all alpha diversity metrics. I...

@mataton Thanks! I have made the edits you suggested.

Let me merge this PR and move on.

Hello @mortonjt This is amazing design! One question: if `ProteinEmbedding` is a subclass of `Protein`, then it must contain the sequence. This might be less flexible if we only want...

There are certainly uses cases for non-protein sequences. For example, the RNA secondary structure is directly related to how 16S primers were designed. In a genome annotation task, proteins are...