Does scikit-bio support phylogenetic tree construction?

Yes, it includes algorithms for tree construction such as Neighbor Joining (NJ) and UPGMA, plus tools for tree manipulation and distance calculations.

Can I use this skill for microbiome diversity analysis?

Yes, the skill provides extensive support for alpha diversity (richness, Shannon) and beta diversity (Bray-Curtis, UniFrac), along with statistical tests like PERMANOVA.

Is it compatible with standard Python data science libraries?

Absolutely. scikit-bio is built to integrate seamlessly with NumPy, Pandas, and Scikit-learn, allowing for robust data science and ML workflows.

What types of biological sequences can scikit-bio handle?

scikit-bio provides specialized, validated classes for DNA, RNA, and Protein sequences, as well as a generic Sequence class for data without specific alphabet restrictions.

Which bioinformatics file formats are supported?

It supports over 19 formats, including common ones like FASTA, FASTQ, GenBank, Newick, and BIOM for feature tables.

Scikit-bio Bioinformatics Toolkit

Name: Scikit-bio Bioinformatics Toolkit
Author: x-cmd

byx-cmd

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Data Science & ML

Analyzes biological data using specialized tools for sequence manipulation, phylogenetics, and microbial ecology metrics.

About

scikit-bio is a comprehensive Python library designed for complex bioinformatics tasks, ranging from sequence alignment and phylogenetic tree construction to multivariate statistical analysis for microbiome research. It enables developers to handle specialized biological file formats like FASTA and Newick, calculate ecological diversity metrics, and perform advanced ordination techniques, making it an essential tool for biological researchers and data scientists working with genomic or community ecology data within an AI-assisted coding environment.

Key Features

8 GitHub stars
Ecological diversity analysis including alpha/beta diversity and UniFrac distances.
Phylogenetic tree construction and manipulation including Neighbor Joining and UPGMA.
Pairwise and multiple sequence alignment using Smith-Waterman and Needleman-Wunsch.
Robust I/O support for over 19 biological file formats including FASTA, FASTQ, and BIOM.
Comprehensive biological sequence manipulation for DNA, RNA, and protein data types.

Use Cases

Constructing evolutionary trees and calculating phylogenetic distances from genetic data.
Processing and converting high-throughput sequencing data between different bioinformatics standards.
Analyzing microbial community composition and diversity in microbiome research projects.

About

Key Features

8 GitHub stars
Ecological diversity analysis including alpha/beta diversity and UniFrac distances.
Phylogenetic tree construction and manipulation including Neighbor Joining and UPGMA.
Pairwise and multiple sequence alignment using Smith-Waterman and Needleman-Wunsch.
Robust I/O support for over 19 biological file formats including FASTA, FASTQ, and BIOM.
Comprehensive biological sequence manipulation for DNA, RNA, and protein data types.

Use Cases

Constructing evolutionary trees and calculating phylogenetic distances from genetic data.
Processing and converting high-throughput sequencing data between different bioinformatics standards.
Analyzing microbial community composition and diversity in microbiome research projects.