bio-comparative-genomics-ancestral-reconstruction
Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-stat
npx skills add BioTender-max/awesome-bio-agent-skills --skill ancestral-reconstruction --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: PAML 4.10.7+, IQ-TREE 2.3.6+, GRASP 2024+ (web/CLI), FastML 3.11+, RevBayes 1.2.4+, BayesTraits V4.1+, R 4.4+, ape 5.8+, phytools 2.3+, corHMM 2.9+, geiger 2.0.11+, phangorn 2.12+, RERconverge 0.3.0+, BioPython 1.84+. Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('corHMM')` then `?ancRECON`, `?make.simmap`, `?ace` - CLI: `codeml` (no `--version`; check `paml -h` or examine `Phylip.tre` example), `iqtree2 --version`, `revbayes --version` - Python: `pip show biopython`; check `Bio.Phylo.PAML.codeml` API If code throws `AttributeError`, `ImportError`, missing slot errors on R S4 objects, or PAML `mlc` parsing failures, introspect the installed package (`?` in R, `help()` in Python) and adapt the example rather than retrying. PAML output formats are stable across 4.9 -> 4.10; IQ-TREE's `--ancestral` flag replaced `-asr` in v2.0+. # Ancestral State Reconstruction **"What did this gene / trait / genome look like at an internal node?"** -> Choose the reconstruction framework that matches the data class (sequence / discrete trait / continuous trait / gene content) and the infere
- Version Compatibility
- Algorithmic Taxonomy
- Decision Tree by Experimental Scenario
- Per-Tool Failure Modes
- Long-branch attraction (LBA) at deep nodes
- Epistasis breaking site-independent ASR
- Root placement error cascading to deep ancestors
- BiSSE false-positive in state-dependent diversification
- Parsimony vs ML on asymmetric rates (Felsenstein bias)
- Continuous-trait BM-only model with non-BM evolution
- Alignment error propagating to ASR
- Quantitative Thresholds
- PAML codeml Ancestral Reconstruction
- IQ-TREE2 Marginal Reconstruction
iqtree2 -s alignment.fasta -m MFP --ancestral -o outgroup_taxon -B 1000 -nt AUTO --prefix asr_iqtree or : Node | Site | State | p_A p_R p_N ... (protein) grasp -aln alignment.fasta -tree species.nwk -out grasp_run --inference joint --threads 8 grasp_run/asr.fasta ancestral sequences at every internal node grasp_run/asr_posterior per-site, per-state posterior grasp_run/asr_indels indel posterior per node per gap-block CLI conda install -c bioconda paml iqtree RevBayes via source build (https://revbayes.github.io/download) or homebrew on macOS GRASP from https://github.com/bodenlab/GRASP (Java)
What does the bio-comparative-genomics-ancestral-reconstruction skill do?
Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-stat
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill ancestral-reconstruction --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.