Generate scheduler-aware phylogenomics workflows from genome assemblies.
npx skills add https://github.com/brunoasm/my_claude_skills --skill busco-phylogeny
Please help me install this Agent Skill. Skill: busco-phylogeny Source: https://github.com/brunoasm/my_claude_skills/tree/main/phylo_from_buscos Command: npx skills add https://github.com/brunoasm/my_claude_skills --skill busco-phylogeny
Phylogenomic analysis is a complex, multi-step process requiring specialized bioinformatics tools and often High-Performance Computing (HPC) expertise. This Skill automates the entire workflow, from raw genome input to final phylogenetic trees and a draft methods section, saving researchers significant time and reducing potential errors.
Generate a phylogeny from 20 insect genome assemblies for a SLURM cluster.
High-intent search queries and answers about installing and using this skill.
Build phylogenetic trees from genome assemblies by running this Skill, which automates ortholog identification via BUSCO, alignment with MAFFT, trimming, concatenation, and phylogenetic inference using IQ-TREE or ASTRAL to produce both concatenated and coalescent trees.
Yes, this Skill generates scheduler-specific scripts for SLURM, PBS, cloud, and local environments, automatically optimizing parallelization and resource allocation for your HPC infrastructure without manual script writing.
The pipeline accepts mixed inputs: local genome assemblies and NCBI accessions, downloading remote genomes via NCBI Datasets CLI and processing them uniformly through the complete phylogenomics workflow.
Yes, it supports multiple trimming strategies—Aliscore/ALICUT, trimAl, BMGE, and ClipKit—plus quality control and recommendations, producing publication-ready alignments and a draft methods section.
Concatenated trees combine all aligned sequences into one supermatrix for IQ-TREE inference; coalescent trees build gene trees per locus then reconcile them with ASTRAL, handling incomplete lineage sorting and producing species trees with different topological assumptions.
No, this Skill automates the entire workflow from genome input to trees and publication text, eliminating the need to manually orchestrate BUSCO, alignment, trimming, concatenation, and phylogenetic inference across your computing environment.
I-OnlabsAutomate phylogenomic workflow design from genome assemblies to trees using BUSCO single-copy orthologs.
hxk622Analyze and manipulate phylogenetic trees in Newick and NHX formats.
Yezez9Align biological sequences with MAFFT and infer evolutionary trees using IQ-TREE 2 or FastTree.
jackspaceManipulate phylogenetic trees with Newick, NHX, PhyloXML, and NeXML formats.
