datasnakes / datasnakes/OrthoEvolution
Alignment Class
Open
@grabear is already working on this.
Since Sep 15, 2017.
:zzz: Status: On Hold :zzz:
Priority: High :fire::fire::fire:
Type: Feature 🔑
- Dominant language
- Python
- Stars
- 28
- Forks
- 5
- Avg merge
- 23m
- Merged PRs (30d)
- 3
Description
Decide on different alignment strategies that we would like to be able to employ.
- Filtered Sequence Alignment
- Amino Acid Alignment with multiple GUIDANCE2 iterations.
- Nucleic Acid Alignment without filtered sequences using PAL2NAL.
- Catch PAL2NAL errors and remove sequences that aren't working
- Employ the Filtered Column Alignment strategy for the sequences that aren't working by aligning multiple query sequences (Homo_sapiens, Macaca_mulatta, Mus_musculus) with the "bad" sequences.
- Catch PAL2NAL errors and remove sequences that aren't working
- Solitary Alignment
- CLUSTAL Omega
- PAL2NAL
- Filtered Column Alignment
- For sequences that are more cluttered, deploy a strategy for safely removing "bad" columns from the alignments by using GUIDANCE2
- Use PAL2NAL on what's left.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
This issue has not been assessed yet.