bionim

This package tries to provide a lot of the most useful data structures and alogrithms need in the different subfield of bio informatics

Pure Nim score 15/100 · tests present · no docs generated

Summary

Latest Version Unknown
License UNLICENSE
CI Status Failing
Downloads 0
Last Indexed 2026-07-21 05:23

Tags

bioinformatics needleman wunsch needleman-wunsch biology

Installation

nimble install bionim
choosenim install bionim
git clone https://github.com/Unaimend/bionim

OS Compatibility

Platform Linux macOS Windows FreeBSD OpenBSD NetBSD Android iOS WASM Embedded
bionim ✓ ✓ ✓ - - - - - - -

Source

Repository https://github.com/Unaimend/bionim
Homepage https://github.com/Unaimend/bionim
Registry Source nimble_official

README

Bionim

test

This package tries to provide a lot of the most useful data structures and algorithms needed in the different subfields of bioinformatics

The apis for most of the algorithms we be quite unstable until version 1.0.0 is reached, also this package will grrow quite a lot in the next few months

Instalation

Requires Nim to be installed on your system. See https://nim-lang.org/

Installation with the nimble package manager is recommended:

nimble install bionim

Tests

To run test just run nimble test in the bionim directory

File Types

  • FASTA Alignments, those are fasta files with added constraint that all sequences must be of the same length
  • General FASTA Files
  • Reading FastQ files

Currently implemented algorithms and data structures

Alignment

Algorithms and data structures usefull in the alignment of genomic and protein based sequences. ## Algorithms * Needleman-Wunsch Basic algorithm used for global alignment * Smith-Waterman Basic algorithm used for local alignment.

Phylogenetics

  • Fitch's algorithm for constructing phylogenetic trees from aligned sequences.

Assembly

  • DeBruijn Graph building and rendering
  • Paired-End DeBruijn grap building and rendering

Documentation

All algorithms and data structures are documented in the projects wiki. Documentation for PhylogeNi and bio_seq can be found on their respective git hub readme's

Credits

In this section are all packages listed on which bionim depends and which were not created by me. * PhylogeNi A library for working with phylogenetic trees * bio_seq A library for working with bioinformatic sequence types

Contributions

If you want to contribute or think that a specific algorithm or data structure should be included in this package just create an issue. Also I am always happy if someone suggest code improvements and stuff like that.

Contact

If you have any questions or just want to contact me regarding this package. Please write to Unaimend+bionim@gmail.com

Todo

Parsing

  • FASTQ parsing

Alignment

  • Calculation of all possible optimal alignment for Needleman-Wunsch
  • Usage of similiarity matrices in Needleman-Wunsch
    • Customizable gap penalties for Needleman-Wunsch

Minimum skew problem