Demonstration of the UPGMA hierarchal clustering algorithm in Pandas, Seaborn, and Scipy
Phylogenetic Insights from Turtles, Lizards, Crocodiles and Birds Sequences. Jupyter Notebook with tree construction
Phylogenetic tree manipulating with Python
🍀 bioseq - a Python package to handle biological sequences and perform common Bioinformatics operations.
UPGMA Algorithm in C++
An end-to-end scRNA-seq analysis pipeline processing raw PBMC data through QC, dimensionality reduction, and clustering, deployed as an interactive, production-ready R Shiny dashboard.
C++ tool for constructing phylogenetic trees from DNA sequences using NJ, UPGMA, Fitch-Margoliash and Minimum Evolution algorithms
从一段 DNA，长出一棵树。浏览器内系统发生树工作室 — FASTA → 距离矩阵 → NJ/UPGMA → 可探索的进化树
Project for the master course: Introduction to bioinformatics
From-scratch molecular-phylogenetics algorithms in R — pairwise alignment, TN93 evolution simulation, UPGMA, Felsenstein likelihood, and independent contrasts, each with passing RUnit tests.
A simple PHP library to build phylogenic trees from distance matrix
A complete SSR population genetics toolkit for any species. Includes data cleaning, UPGMA clustering, PCoA, STRUCTURE formatting, STRUCTURE barplot visualization, and supporting scripts for reproducible microsatellite population analyses.
UPGMA hierarchical clustering algorithm constructing rooted ultrametric phylogenetic trees from pairwise evolutionary genetic distance matrices.
[Python] Construction of SARS-CoV-2 Phylogenetic Tree.
A Python toolkit for simulating sequence evolution and exploring molecular clock algorithms
Repository for Computational Biology course at ETH Zürich
Python · pairwise alignment · dN/dS · UPGMA phylogeny — Genomic surveillance for Cotton Leaf Curl Virus on real NCBI GenBank sequences: which variant is rising and is that real, is anything selecting for it, and how are strains related. Collapsing clonal duplicates turned 9 'emerging variants' into 0. 101 tests, zero dependencies.
UPGMA clustering of constructing phylogenetic relationships implemented from scratch
Sequence alignment and phylogeny of SARS-CoV-2 genomes — Needleman-Wunsch, Smith-Waterman, UPGMA and Neighbor-Joining implemented from scratch in Python
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