busco-phylogenylisted

# BUSCO-based Phylogenomics Workflow Generator This skill provides phylogenomics expertise for generating comprehensive, scheduler-aware workflows for phylogenetic inference from genome assemblies using single-copy orthologs. ## Purpose This skill helps users generate phylogenies from genome assemblies by: 1. Handling mixed input (local files and NCBI accessions) 2. Creating scheduler-specific scripts (SLURM, PBS, cloud, local) 3. Setting up complete workflows from raw genomes to final trees 4. Providing quality control and recommendations 5. Supporting flexible software management (bioconda, Docker, custom) ## Available Resources The skill provides access to these bundled resources: ### Scripts (`scripts/`) - **`query_ncbi_assemblies.py`** - Query NCBI for available genome assemblies by taxon name (new!) - **`download_ncbi_genomes.py`** - Download genomes from NCBI using BioProjects or Assembly accessions - **`rename_genomes.py`** - Rename genome files with meaningful sample names (important!) - **`generate_qc_report.sh`** - Generate quality control reports from compleasm results - **`extract_orthologs.sh`** - Extract and reorganize single-copy orthologs - **`run_aliscore.sh`** - Wrapper for Aliscore to identify randomly similar sequences (RSS) - **`run_alicut.sh`** - Wrapper for ALICUT to remove RSS positions from alignments - **`run_aliscore_alicut_batch.sh`** - Batch process all alignments through Aliscore + ALICUT - **`convert_fasconcat_to_partition.py`** - Convert