python-alignment

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Documentation

1

Does anyone know whether there is any documentation available on the full functionalities? Maybe someone has something local that he/she is willing to share? So far, I only found the...

MaximMoinat

`'-'` as a gap element doesn't work for my project. Currently, I am doing the following, but it seems pretty hack-ish: ```python import alignment alignment.vocabulary.GAP_ELEMENT = '∅' ``` This pull...

reynoldsnlp

Long sequences run into RecursionError

4

Since `backtraceFrom` is implemented by recursion (instead of iteration), calling the aligner on "long" sequences (more than 1000 items) results in a `RecursionError` with Python defaults. Extending stack depth limit...

bertsky

I am not sure whether there even exists a metric for this: if there is a segment where both sequences deviate a lot in their length, then the current algorithm...

bertsky

Unlimited backtrace is impractical

1

When globally aligning sequences that deviate much, combinatory explosion can quickly leed to excessive runtime memory consumption in the current implementation. And it is not always easy to detect those...

bertsky

This isn't ready yet. I've re-implemented the Smith Waterman algorithm in a non-recursive way. It creates _SequenceAlignment_ only once but still supports multiple alignments. It would probably be good to...

de-code

Algorithm details

6

Hi, Thank you for providing the module. I was wondering whether you could provide information on the algorithms used? e.g. Smith Watermann? (While your code is well structured I am...

de-code

Multiple sequence alignment?

1

Any thoughts or future plans on incorporating multiple sequence alignment algorithms? P.S. really found your library useful :smile:

rodricios