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Need capability to manipulate a multiple sequence alignment, seems like the right place to put it.
I started working on this but it may need more thought about how it will play nice with the pairwi…
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Two users have reported similar errors with this tool: The MAF source specified (xx) appears to be invalid.
- https://help.galaxyproject.org/t/help-extracting-pairwise-alignments-from-mafs/5481
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I was reading through the FAQs and didnt see anything about MSAs. Can diamond do MSAs? or just pairwise alignments?
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Dear Beliveau Lab,
When running the PaintSHOP pipeline using the standard example run but changing the length of probes (to 20mers) causes the sam2pairwise to exit due to finding unmapped reads whi…
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I've found the following problem/error in scikit-bio 0.5.5 (Python 3.6.7): `aligned_query_sequence` and `aligned_target_sequence` has different lengths for some alignments (using StripedSmithWaterman)…
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The WFA (and related BiWFA) algorithm have provided some really nice asymptotic and practical advances for pairwise alignment under a set of realistic scoring functions. Do you have any thoughts on t…
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## Platform
- SeqAn version: 3
- Operating system: `Linux raptor.ucsd.edu 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:51:45 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux`
- Compiler: gcc (Ubu…
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Hi,
Quite impressed with the speed at which mmseq performs pairwise alignments. Have a couple of questions:
1. Can i perform alignments using sequences with degenerate characters? Right now the…
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Dear author, multiz is a very useful software. However, at present, I need to merge more genomes, according to the pairwise merger speed is too slow, is there any way to improve the merger speed? Than…
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I am testing edlib for the purpose of calculating pairwise identites between sequences, using the BLAST/USEARCH definition of sequence identity; i.e. $\text{id} = \frac{\text{edit distance}}{\text{ali…