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search the node in the tree with the closest sequence. In general, this requires pairwise alignment. I implemented a banded pairwise alignment here:
https://github.com/neherlab/timetree_viewer/blob/ma…
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## This is a practical guidance for generating the most conserved elements of drosophila simulans
- [ ] Prepare the working directory.
- [ ] Prepare the genome data.
- [ ] Set the follow…
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This class should store two `GrammaredSequence` objects, the pairwise alignment score, and the start/end positions of the respective sequences. This class should have a `to_tabular_msa` method to conv…
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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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Hello,
I am a pHD student in Bioinformatics at the University of Toledo. While my work focuses mainly on Neuroscience, I work with all different times of omics data sets. I would like a video on Se…
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Hello,
I ran the perl script. The script runs till the following message is displayed:
Reported 91 pairwise alignments, 100 HSSPs
91 queries aligned.
#3
and terminates
I can't locate my out…
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Hi,
I am doing all-vs-all pairwise alignment of filtered ONT reads (phred score > 9). Due to extensive memory usage, I have to split reads into 10,000 reads per file, which is about 140 MB. Yet, i…
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The docstring of `ScipyDist` describes a `colalign` argument which can be set to align columns of the same name in `X`, `X2` before the distance is computed.
Unfortunately, this is not actually don…
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I see the first instance of an actor in `pony-bio` as being an implementation of multiple sequence alignment (MSA) after #13 is addressed
Such an actor would be initialized with the MSA parameters …
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Hello,
I'm testing dust3r with the Lego dataset using known camera poses to determine if this improves the (world-coordinate) pointmap generation during the global alignment optimization process. I…