Skill UI

Biopython is a comprehensive Python library designed for molecular biology and bioinformatics. It provides powerful tools for sequence manipulation (DNA, RNA, Protein), parsing standard biological file formats (FASTA, GenBank, PDB), accessing external databases like NCBI (PubMed, GenBank) via Entrez, and performing complex analyses such as sequence alignment, phylogenetic tree construction, and structural bioinformatics. Ideal for building robust, automated bioinformatics pipelines.

BioServices is a comprehensive Python library providing programmatic access to over 40 major bioinformatics web services and databases (e.g., UniProt, KEGG, ChEMBL). It is designed for complex biological data workflows, enabling cross-database querying, identifier mapping across diverse biological resources, and advanced sequence/pathway analysis in a single, consistent API structure.

gget is a comprehensive command-line interface and Python library providing unified access to over 20 major bioinformatics databases. It allows researchers to perform complex tasks such as gene information retrieval, sequence analysis (BLAST, BLAT), structural modeling, and enrichment analysis using a consistent API. Ideal for interactive data exploration, quick lookups, and integrating bioinformatics workflows into Python scripts.

This skill provides comprehensive tools for analyzing and engineering protein glycosylation patterns. It scans sequences for canonical N-glycosylation sequons (N-X-S/T), predicts O-glycosylation hotspots, and supports rational modification. It is essential for optimizing therapeutic antibodies, improving protein stability, or designing complex vaccine antigens.

Gtars is a comprehensive, high-performance toolkit written in Rust, featuring Python bindings for advanced genomic interval analysis. It is designed for computational biology and machine learning applications, providing specialized modules for overlap detection (IGD), coverage track generation (WIG/BigWig), genomic tokenization, and single-cell fragment analysis. Use it for processing BED files, validating reference sequences, and building robust bioinformatic pipelines.

This comprehensive toolkit facilitates the entire phylogenetic analysis workflow, from sequence alignment to tree inference. It integrates industry-standard tools like MAFFT for multiple sequence alignment, TrimAl for alignment trimming, and powerful maximum likelihood methods using IQ-TREE 2 or FastTree. Ideal for molecular genomics, tracing viral phylodynamics, studying protein evolution, or conducting molecular clock analysis. Built using Python for seamless integration.

Pysam is a powerful Python module designed for reading, manipulating, and writing core genomic file formats. It provides a Pythonic interface to htslib, enabling users to process alignment files (BAM/CRAM), variant calls (VCF/BCF), and reference sequences (FASTA/FASTQ). Use it for implementing complex bioinformatics pipelines, calculating coverage, quality control, and detailed variant annotation.

scikit-bio is a comprehensive Python library designed for advanced bioinformatics and biological data analysis. It provides robust tools for sequence manipulation (DNA, RNA, Protein), performing sophisticated sequence alignments (global, local, multiple), constructing and analyzing phylogenetic trees, and conducting complex ecological statistics. Key features include calculating diversity metrics (alpha/beta), running ordination analyses (PCoA), and handling diverse biological file formats (FASTA, Newick, BIOM). Ideal for researchers in microbiology, genomics, and ecology.