bio-comparative-genomics-gene-tree-species-tree-reconciliation

npx skills add BioTender-max/awesome-bio-agent-skills --skill gene-tree-species-tree-reconciliation --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## Version Compatibility Reference examples tested with: ALE 1.0+ (ssolo/ALE github), GeneRax 2.1.3+ (BenoitMorel/GeneRax), AleRax 1.2.0+ (BenoitMorel/AleRax; Morel 2024 Bioinformatics 40:btae162), Whale.jl 2.0+ (arzwa/Whale.jl), RANGER-DTL 2.0+ (Bansal lab; Bansal 2018 Bioinformatics 34:3214), NOTUNG 2.9.1.5+ (Stolzer 2012; Chen 2000), ecceTERA 1.2.5+, Treerecs 1.2+, IQ-TREE 2.3.6+, MrBayes 3.2.7+, BUSCO 5.7+, ete4 4.1.0+, BioPython 1.84+. Open Tree of Life and NCBI Taxonomy reference databases at 2024-Q3 minimum for species-tree-aware inference. Before using code patterns, verify installed versions match. If versions differ: - CLI: `ALEml_undated --help`, `ALEml --help` (dated), `generax --help`, `alerax --help` - Julia: `using Whale; Whale.WhaleProblem`; `]status` for package versions - Python: `pip show ete4`; `ete4 --help` If code throws `species tree mismatch`, `gene tree taxa not in species tree`, or `MPI process pool failure`, these reconciliation tools share strict label-consistency requirements: species labels must match exactly across the species tree and gene trees (case-sensitive, no whitespace), and gene IDs typically encode species via prefix (`species|gene_id` separ

for tree in gene_trees/*.nwk; do
sed -i 's/_gene_/|/g' "$tree"   # adjust separator
done
mkdir -p gene_trees
for og in orthogroups/*.fa; do
iqtree2 -s $og -m TEST -B 1000 -nt 2 --prefix gene_trees/$base
for ufb in gene_trees/*.ufboot; do
ALEobserve $ufb
Produces gene_trees/*.ale files
mkdir -p reconciled