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**This does not handle gap characters**
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Zeros in first row and first column
Max value in last row or last column is end of alignment
srp = re.search(r'(?= {scorethr}
AND mirna IN (…
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**Add function for plotting phylogenetric trees**
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Use turtle to generate a phylogenetic tree from a distance matrix
This is a speed optimization - directly reference position
instead of searchi…
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**This does not handle gap characters**
----
Zeros in first row and first column
Max value in last row or last column is end of alignment
srp = re.search(r'(?= {scorethr}
AND mirna IN (…
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The Edgar 2016 paper _says_ UNOISE2 used the Levenshtein distance: https://www.biorxiv.org/content/10.1101/081257v1.full
Comment https://github.com/torognes/vsearch/pull/283#issuecomment-360850868 …
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Anyone up to getting Needleman-Wunsch and Smith-Waterman written in cython? The current all-python versions in pyCogent are super slow and the nwalign package has a severe memory leak issue.
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Hello,
I am doing a test of patchwork using a genome assembled in SPades as a query with a large ortholog set as a reference.
Patchwork shoots me an error after the alignment trimming step I canno…
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Use the COVID genome sequence dataset to test different behaviors of alignment algorithms. Should pay attention to different alignment results, time and memory usage.
- [x] Obtain the COVID genome …
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Below is the list of to-dos from 28th, Feb, 2022 to 6th, Mar, 2022.
- [x] Fork and clone [cogent3](https://github.com/cogent3/cogent3) and [c3dev](https://github.com/cogent3/c3dev) repositories to lo…
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The Needleman-Wunsch implementation is incorrect. The example in the documentation is properly selected because it is probably the only one for which it finds the optimal alignment :wink:.
Example…
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Is it possible two calculate the DTW distance by other distance metric than euclidean. For example: I have two time series sequence of strings as follows:
`a = ['rain', 'sunny', 'rain', 'cloudy']`
…