Over the past year, I've spent a great deal of time working on several packages related to bioinformatics. Of those packages, the two that I believe have the most relevance to this forum are Goombay and Biobase.
Goombay
Goombay is my sequence alignment python package. It has over 20 algorithms including classics like Needleman-Wunsch, Smith-Waterman, and Waterman-Smith-Beyer, as well as some more niche algorithms such as MLIPNS, Ratcliff-Obershelp, and Hamann. This package has everything from pairwise global and local alignments to multiple sequence alignment with Feng Doolittle. Currently, the Notredame-Higgins-Heringa MSA algorithm is being worked on to be added to the algorithms in this package. The philosophy of the package is to have a unified interface for users and prioritization of ease of use. I have a few Jupyter Notebook examples of this package being used in practice in concert with my other Python package Biobase.
Biobase
Biobase started off as my pet project to keep biological constants and algorithms that I needed to solve Rosalind problems, but it has ballooned into a full on python package. It includes substitution matrices, biological constants such as codon tables and protein IUPAC names, and also includes some basic functions for sequence analysis. The most recent additions to this package were by a contributor who added both an ORF finder and a DNA entropy calculator.
Goombay
Goombay is my sequence alignment python package. It has over 20 algorithms including classics like Needleman-Wunsch, Smith-Waterman, and Waterman-Smith-Beyer, as well as some more niche algorithms such as MLIPNS, Ratcliff-Obershelp, and Hamann. This package has everything from pairwise global and local alignments to multiple sequence alignment with Feng Doolittle. Currently, the Notredame-Higgins-Heringa MSA algorithm is being worked on to be added to the algorithms in this package. The philosophy of the package is to have a unified interface for users and prioritization of ease of use. I have a few Jupyter Notebook examples of this package being used in practice in concert with my other Python package Biobase.
Biobase
Biobase started off as my pet project to keep biological constants and algorithms that I needed to solve Rosalind problems, but it has ballooned into a full on python package. It includes substitution matrices, biological constants such as codon tables and protein IUPAC names, and also includes some basic functions for sequence analysis. The most recent additions to this package were by a contributor who added both an ORF finder and a DNA entropy calculator.
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