I am currently working on verifying the subgenotyping of our sequences and a subsample from the Los Alamos NL database. My supervisor has recommended using REGA & COMET for this purpose. While our dataset, which consists of slightly > 1,000 sequences, can be easily subgenotyped using the online versions of these tools, the LANL dataset is significantly larger, prompting me to consider local installations. Unfortunately, however, I have been unable to find the source repositories for REGA & COMET.
I did come across a link to the entire REGA DB but I am unsure if it contains the subgenotyping tool or if the last can be installed separately. I am also interested in exploring other locally installable tools of comparable quality.
In my search, I found jpHMM, which is available for download and free use. However, it seems to be less frequently used in publications compared to the aforementioned ones.
I would appreciate any insights on the quality of jpHMM or any other recommended tools for local installation (even as packages, e.g. for Python).
If you have experience with these subgenotyping tools or any relevant advice, please share your thoughts! Your help is greatly appreciated!