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hla-b27-phylogeny

This repository stores the code for my research about the inference of the likelihood of ankylosing spondylitis based on the clade of HLA-B27 phylogenetic tree.

https://github.com/undemalum/hla-b27-phylogeny

Science Score: 44.0%

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    Low similarity (9.1%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

This repository stores the code for my research about the inference of the likelihood of ankylosing spondylitis based on the clade of HLA-B27 phylogenetic tree.

Basic Info
  • Host: GitHub
  • Owner: undeMalum
  • License: mit
  • Language: Python
  • Default Branch: main
  • Size: 393 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created over 2 years ago · Last pushed about 1 year ago
Metadata Files
Readme License Citation

README.md

HLA-B27 Phylogeny

HLA-B27 Phylogeny is my research project where I attempt to determine whether the clade (a group of alleles that have evolved from a common ancestor/allele) of the HLA-B27 alleles phylogenetic tree is a reasonable predictor of the ankylosing spondylitis occurrence. More details will be available in my research paper, which I will not link now since I use it at my Biology Internal Assessment in IBDP.

Therefore, to avoid violating academic integrity, here's my candidate number to prove the code I reference in my work is actually mine.

Candidate number: kyz635

Projects structure

  • phylo_trees: contains the trees I created
    • phyloxml: trees in phyloxml format
    • png trees as png images
  • sequences: contains non-aligned sequences - both downloaded and modified
  • alignments: contains aligned sequences
  • src: contains the code I used to process sequences and create trees
    • modyfing_sequences: code for preprocessing data: changing headings, joining sequences, making letters capital etc.
    • phylogenetic_tree: code for creating and displaying trees

Tools

Check out requirements.txt for the libraries I used. However, the most important are biopython for almost all the work and matplotlib for displaying trees (biopython dependency.)

Contribute

If you would like to contribute, just fork this repository, make some changes, and open pull request. Any contributions are welcomed!

Owner

  • Name: Mateusz Konat
  • Login: undeMalum
  • Kind: user
  • Location: Poznań, Poland

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: HLA-B7 Phylogeny
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Mateusz Konat
    email: mateusz.konat.py@gmail.com
repository-code: 'https://github.com/undeMalum/hla-b27-phylogeny'
abstract: >-
  This repository contains the code for my research on
  inferring the likelihood of ankylosing spondylitis based
  on the given clade of the HLA-B27 phylogenetic tree.
keywords:
  - python
  - phylogeny
  - hla-b27
license: MIT
commit: ' b3fdcc3'

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Dependencies

requirements.txt pypi
  • Pillow ==10.1.0
  • biopython ==1.81
  • contourpy ==1.2.0
  • cycler ==0.12.1
  • fonttools ==4.46.0
  • kiwisolver ==1.4.5
  • matplotlib ==3.8.2
  • numpy ==1.26.2
  • packaging ==23.2
  • pyparsing ==3.1.1
  • python-dateutil ==2.8.2
  • six ==1.16.0