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# Background
The JnJ team requested using [Mafft](https://mafft.cbrc.jp/alignment/server/index.html) for DNA/RNA sequence alignment.
# Scope of work
* Implement running MSA via Mafft
* Add UI to…
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It would be useful if there was a function that automatically did pairwise alignment for all sequences in a list creating a new data structure that contained:
(1) an identity matrix (or distance)
(2)…
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Using the attached alignment and this code within a jupyter notebook
```python
from cogent3 import get_app, load_aligned_seqs
aln = load_aligned_seqs("ENSG00000000971.fa", moltype="dna")
phylo…
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I have a set of nucleotide sequences and I need the pairwise sequence similarity of all vs all.
I understand that one should create a fake_pref and use it to run mmseqs align. Yet, in the document…
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**Python script that performs alignment based on user input**
**2.25/8**
| Exercise | Points Possible | Grade |
| -------- | ------- | ------- |
| Read in inputs | 2 | 1.5 |
| Initialize ma…
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The option to remove sequences using -seqoverlap and -resoverlap produces results I find unexpected. From what I can tell, it seems that when -resoverlap compares if a residue is the same in the other…
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**Python script that performs alignment based on user input**
**7.75/8**
| Exercise | Points Possible | Grade |
| -------- | ------- | ------- |
| Read in inputs | 2 | 2 |
| Initialize matr…
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### Contribution guidelines
- [X] I've read the [contribution guidelines](https://github.com/squidfunk/mkdocs-material/blob/master/CONTRIBUTING.md) and wholeheartedly agree
### I've found a bug and …
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**Python script that performs alignment based on user input**
**0/8**
| Exercise | Points Possible | Grade |
| -------- | ------- | ------- |
| Read in inputs | 2 | 2 |
| Initialize matrice…
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### Description of feature
The current stop-codon detection in ampliseq could be improved and supplemented with frame-shift detection by implementing [MACSE](https://doi.org/10.1093/molbev/msy159). T…