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Added reference to https://github.com/stanfordnlp/string2string, restructured other references
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poke1024 authored May 22, 2023
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Expand Up @@ -4,6 +4,9 @@ Fast and simple alignments in Python:

![Example inside Jupyter](https://github.com/poke1024/pyalign/raw/main/docs/jupyter_example.png)

Make sure to take a look at "other alignment libraries" below to better understand if this is
the right library for you.

<hr>

Alignments have been a staple algorithm in bioinformatics for decades now,
Expand Down Expand Up @@ -175,21 +178,14 @@ The benchmark code can be found under [benchmark.py](demo/py/benchmark.py).

Here is a short overview of other libraries.

## great bio alignment libraries

* https://github.com/jeffdaily/parasail
* https://biopython.org/docs/latest/api/Bio.Align.html

## similar to pyalign
## Nice General Purpose Implementations

* https://edist.readthedocs.io/en/latest/
* https://github.com/stanfordnlp/string2string (RECOMMENDED!)
* https://pypi.org/project/textdistance/
* https://github.com/mbreese/swalign/
* https://github.com/seqan/seqan3
* https://github.com/wannesm/dtaidistance
* https://edist.readthedocs.io/en/latest/
* https://github.com/maxbachmann/RapidFuzz

## for large scale problems
## For large scale / bioinformatics problems

What you will *not* find in pyalign:

Expand All @@ -200,9 +196,22 @@ What you will *not* find in pyalign:

If you need any of the above, you might want to take a look at:

* https://pypi.org/project/edlib/
* https://github.com/smarco/WFA2-lib and https://github.com/kcleal/pywfa
* https://github.com/vishnubob/ssw
* https://github.com/lh3/ksw2
* https://github.com/Daniel-Liu-c0deb0t/block-aligner
* https://github.com/jeffdaily/parasail
* https://biopython.org/docs/latest/api/Bio.Align.html
* http://cudasw.sourceforge.net/homepage.htm
* https://blast.ncbi.nlm.nih.gov/Blast.cgi

## Even more alignment libraries

* https://github.com/mbreese/swalign/
* https://github.com/seqan/seqan3
* https://github.com/wannesm/dtaidistance

# References

## Original Works
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