busco-phylogeny

You can automate phylogenomic workflow design by using this Skill to generate scheduler-aware scripts that handle ortholog identification, alignment, trimming, and phylogenetic inference from raw genome assemblies. It applies BUSCO and compleasm to identify single-copy orthologs across multiple genomes.

Building phylogenetic trees from NCBI-accessioned assemblies is streamlined by this Skill, which integrates ncbi-datasets tools to fetch genomes and pipelines them through QC, alignment, concatenation, and inference using IQ-TREE and ASTRAL to produce final trees.

Yes, this phylogenomics workflow supports SLURM and PBS schedulers. It generates scheduler-aware scripts tailored for SLURM, PBS, cloud, or local execution environments, ensuring the phylogenomic pipeline runs correctly on your specific compute infrastructure.

Yes, you need a unified conda environment to run the compleasm and IQ-TREE pipeline. The environment must include compleasm, MAFFT, IQ-TREE, ASTRAL, trimming tools, and Aliscore/ALICUT scripts to execute the end-to-end phylogenomic workflow.

The workflow handles multiple sequence alignment and trimming for phylogenomics by automating MAFFT for alignment and applying dedicated trimming tools alongside Aliscore/ALICUT scripts. This ensures concatenated alignments are clean before phylogenetic inference.

Yes, you can generate publication-ready methods paragraphs from this BUSCO phylogenomics pipeline. The Skill automatically produces ready-to-use methods paragraphs detailing the alignment, trimming, and phylogenetic inference steps for your publications.