-
I am running clustering of DNA sequences which are very similar and with multiple repetitions within the file. The problem is, identical sequences does not cluster together, but rather are spread acro…
-
## Expected Behavior
[dataset.zip](https://github.com/user-attachments/files/16023829/dataset.zip)
I have a group of sequences which is properly aligned with almost full length and >95% identity usi…
-
Hi,
I'm having difficulty clustering using profiles when following the instructions in the wiki. Specifically I'm referring to this section:
```
# extract consensus sequences from profiles
…
-
Organize thoughts and outlines with Lesli about data needed for the clustering algorithm. Make sure that the outlines are clear so that we can move forward to Q5 seamlessly. Provide an outline of the …
-
Present meeting: Thomas, Karin, Håkon, Magdalena and Eve (me)
---
- [ ] Prepare next meeting with the rest of the results also available, incl also snps and continue the report
----
- [ ] co…
-
Dear,
I am using mmseqs2 to remove redundant sequences and isoforms from eukaryotic proteomes. However, we obtained some unexpected and undesired clusters and we would like to understand what is g…
-
Preferably just after or before `REMOVE_EXACT_DUPLICATES` so we reduce # sequences going into clustering
-
Hi, I am in the process of building a searchable database of antibody and T cell receptor repertoires (here, a "repertoire" is a set of antibody or TCR sequences from a single blood sample from a sing…
-
Hi,
I am having some trouble using hyperfreq with some samples in which a large percentage of the sequences are hypermutated. I assume it is because of the consensus sequences that they are compared …
-
## By marker type:
- [ ] SNP
- [ ] Sequence
- [ ] Microsatellite
Please refer to the issue number when making a pull request.
## Questions to address:
- What individual based distances exist?
- What …