Results for “phylogenetic-tree”

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

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

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

Botany Based Simulation Skill

Nested Sets

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.

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.

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.

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

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

Applied Botany Synthesis Skill

Create foliage types and place/scatter foliage instances on landscapes and meshes (FoliageService). Use when the user asks to add trees/grass/bushes/rocks as foliage, create a foliage type from a mesh, scatter or paint foliage instances, or query/remove foliage on a surface.

Use when searching protein query sequences against a translated nucleotide database to identify protein-coding regions or homologs in genomic data.

Use when performing multiple sequence alignment on nucleotide or protein sequences, such as preparing alignments for phylogenetic analysis or comparative genomics.

Strategic patterns for solving intractable problems through cascading approximation, self-improvement, and heterogeneous evaluation from DeepMind's AlphaGo system

Runs a relentless interview that asks every frontier question at once, round by round. Use when the user wants to be grilled on a design or map a design tree.

Closure Table

Applied Botany Modeling Skill