Results for “phylogenetic-tree”

Use when inferring maximum-likelihood phylogenetic trees, selecting substitution models, running bootstrap support analyses, or performing partitioned phylogenetic analyses on sequence alignments.

Phylogenetic tree toolkit (ETE). Tree manipulation (Newick/NHX), evolutionary event detection, orthology/paralogy, NCBI taxonomy, visualization (PDF/SVG), for phylogenomics.

Analyze biological sequences, alignments, phylogenetic trees, and diversity metrics (alpha/beta, UniFrac) with ordination (PCoA) and PERMANOVA for microbiome and community ecology data.

A powerful tree component for displaying hierarchical data with features like selection, checking, drag-and-drop, virtual scrolling, async loading, and search filtering.

Use when performing multiple sequence alignments on protein or nucleotide sequences, generating phylogenetic trees, or producing alignment output in various formats.

Use when inferring maximum-likelihood phylogenies from aligned sequences, performing automated model selection, or assessing branch support with bootstrap or aLRT methods

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.

A tree-structured select component for hierarchical data selection with features like multiple selection, checkboxes, filtering, and async loading

Manipulate biological sequences, parse FASTA/GenBank/PDB files, access NCBI databases, run BLAST searches, and perform phylogenetics using the Biopython library.

Botany Based Simulation Skill

A cascader component for displaying and selecting tree-structured data with support for single/multiple selection, async loading, filtering, and various check strategies

Manages vector embeddings with Pinecone for semantic search, recommendation, and RAG pipelines.

Detect splice donor and acceptor sites in DNA sequences using the Genomic Intelligence G0 BigBird transformer, via the hosted /v1/tasks/splice/predict API. Returns per-position site probabilities and called sites.

Nested Sets

Systematic plan stress-testing through relentless one-question-at-a-time decision-tree interviewing

Botany Based Synthesis Skill

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

Flamingo: A Visual Language Model for Few-Shot Learning

Simulates meiotic recombination to produce offspring genomes from parent pairs, modeling Mendelian segregation, de novo mutation, sex determination, trait inference, and clinical evaluation against a disease registry.

Automates genome-wide association studies from genotype files to publication-ready results, running PLINK2 QC and REGENIE regression with Manhattan and QQ plots.

绘制研究领域或技术主题的谱系脉络与历史演进图，可视化思想的演化路径，展示早期工作中的技术难题如何被后续研究逐步解决。当用户想了解某个主题的发展轨迹、某个模型或技术的"家族树"（family tree）、某条研究线索在多年间的演进路线、技术迭代脉络、论文/模型谱系，或询问"X 是如何一步步发展来的""X 解决了前人的什么问题""梳理 X 的发展历史"时触发。产出为嵌入 Mermaid 图表的 Markdown 文件（演进图 + 节点明细表 + 阶段叙事），可直接粘贴至 Mermaid 查看器或提交至代码仓库。

Template do pack (ai-ml/03-rag-pipeline.md). Orienta o agente em integracao de IA/ML, LLM e pipelines de dados alinhado a esse contexto.

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

B-Tree Indexes

Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST/BLAT, viral sequence downloads, AlphaFold structures, enrichment analysis, OpenTargets, COSMIC, CELLxGENE, and 8cube mouse specificity/expression data. Best for interactive exploration and simple queries. For batch processing or advanced BLAST use biopython; for multi-database Python workflows use bioservices.

Performs HLA allele genotyping from WGS/WES VCF data, producing a structured markdown report and machine-readable JSON results.

Botany Analysis Expert Skill

Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.

Applied Virology Design Skill

Train, evaluate, distill, quantize, export, and run inference for PyTorch-based TAO image classification models with support for multiple backbones.

Infer gene regulatory networks from gene expression data using scalable algorithms (GRNBoost2, GENIE3) with support for distributed computation.

Takes pre-computed differential expression results from DESeq2, edgeR, limma, or PyDESeq2 and produces a structured, publication-ready summary with ranked gene lists, biological themes, and key observations.