Michael Alonge

Hi there, RaGOO is no longer supported. Please use [RagTag](https://github.com/malonge/RagTag) instead.

It's definitely time for this. I will keep you posted on progress. Thanks

Hi there, This will be implemented in v2, which will hopefully be released in the next few months. Sorry about the delay!

Hi there, There are two main ways to tell if a sequence was unplaced. First of all, an unplaced sequence will not appear in the first column of `ragtag.confidence.txt`. Also,...

Hi there, I apologize for my delayed response. First of all, I recommend switching your analysis over to RagTag, if at all possible: https://github.com/malonge/RagTag Though ragtag is much improved over...

Hi there, I am happy to give a detailed explanation. First, can you tell me what the grouping confidence score is? That will be in the "groupings" folder. Thanks

Thanks for sharing this. I would say that the grouping and orientation scores look pretty good. The location score is low, though that is perhaps the least descriptive since it...

also, please see the preprint for a better description of the confidence scores: https://www.biorxiv.org/content/10.1101/519637v1

No that is not what I mean. Allow me to clarify. By default, each contig is placed exactly once, unaltered, in the final ragoo.fasta file. So the final file represents...

No problem. I will respond again to this issue when I have made the alignment length a tunable parameter.