bio-comparative-genomics-hgt-detection

What this skill does

## Version Compatibility

Reference examples tested with: HGTector 2.0b3+, AvP 1.0.4+, HGTphyloDetect 1.0+, ALE 1.0+ (ssolo/ALE github), GeneRax 2.1.3+, AleRax 1.2.0+ (Morel 2024), RANGER-DTL 2.0+, IslandViewer 4 (web), mobileOG-db 1.0+, MetaCHIP 1.10+, IQ-TREE 2.3.6+, BioPython 1.84+, DIAMOND 2.1.10+. Open Tree of Life and NCBI Taxonomy reference databases updated 2024-Q3 minimum for HGTector/AvP.

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show hgtector` then `hgtector search --help`
- CLI: `ALEml_undated --help`, `generax --help`, `alerax --help`
- DB: `hgtector database --check` for taxonomy version

If code throws `Taxonomy ID not found`, `database version mismatch`, or `KeyError` on NCBI taxids, refresh the local taxonomy dump (NCBI updates monthly). ALE/GeneRax expect newick gene trees with bootstraps; AleRax expects gene-tree distributions (uniform bootstrap samples or UFBoot trees).

# Horizontal Gene Transfer Detection

**"Are these genes horizontally acquired, and from where?"** -> HGT signal lives in three orthogonal signal classes: composition (recent transfers carry donor codon usage; erodes by Lawrence-Ochman 1998 amelioration in ~50-200 Myr), phylogeny (gene tree nests within distant clade), and phyletic distribution (patchy taxonomic presence). No single class proves HGT; **claims require concordance across at least two classes** plus mandatory exclusion of contamination and differential gene loss (DGL). The most consequential failure mode in eukaryotic HGT detection is contamination passing all three classes silently (Boothby 2015 tardigrade retraction; Crisp 2015 human "145 HGTs" refuted by Salzberg 2017 GBE 9:1869).

- Python: `hgtector search` -> `hgtector analyze` for BLAST-distribution screen
- Python: `AvP` (Koutsovoulos 2022 PLoS Comp Biol 18:e1010686) for eukaryotic phylogenetic HGT with automated tree workflow
- CLI: `ALEml_undated` (Szöllősi 2013 Syst Biol 62:901), `generax` (Morel 2020 MBE 37:2763), `alerax` (Morel 2024 Bioinformatics 40:btae162) for prokaryote DTL reconciliation
- Web: IslandViewer 4 (Bertelli 2017 NAR 45:W30) for bacterial genomic islands
- CLI: `metachip` (Song 2019 Microbiome 7:36) for metagenomic HGT inference

## Algorithmic Taxonomy

| Method class | Tool | Signal | Strength | Fails when |
|--------------|------|--------|----------|------------|
| Composition (parametric) | SIGI-HMM (Waack 2006 BMC Bioinf 7:142) | HMM on codon-usage anomaly | Recent transfers (<50 Myr); single-locus resolution | Amelioration eroded composition; native composition heterogeneous (Streptomyces, Borrelia) |
| Composition (parametric) | AlienHunter (Vernikos & Parkhill 2006 Bioinformatics 22:2196) | Variable-window tetranucleotide IVOM | Recent island detection; window-size aware | Old transfers; high-variance native composition |
| Composition (parametric) | IslandPath-DIMOB (Bertelli 2017) | Dinucleotide bias + mobility genes | Combines composition + mobile-element signature | Mobile-element-free transfers |
| Composition aggregator | IslandViewer 4 web (Bertelli 2017 NAR 45:W30) | Consensus of IslandPath / SIGI / IslandPick | Best single-genome bacterial screen; curated benchmark | Recent radiations; close-relative donors |
| BLAST-distribution | HGTector v2 (Zhu 2020 Bioinformatics 36:i538) | Close vs distal BLAST hit ratio against full taxonomy | No tree required; scales to thousands of genomes | Close-relative donors (similar lineage hits); incomplete taxonomic sampling |
| BLAST-distribution | DarkHorse (Podell & Gaasterland 2007 GB 8:R16) | Lineage Probability Index (LPI) | Quantifies taxonomic prior of best hits | Same lineage-coverage caveat as HGTector |
| BLAST-distribution | Alien Index (Gladyshev 2008 Science 320:1210; recent: AI tools) | Best hit metazoan vs non-metazoan score | Standard for eukaryote HGT screen | False positives from rapid evolution / contamination |
| Phylogenetic incongruence | AvP (Koutsovoulos 2022) | Automated tree-building + AU test on candidate HGTs | End-to-end eukaryote pipeline; orthogroup-aware | Poor taxon sampling at putative donor lineage |
| Phylogenetic incongruence | HGTphyloDetect (Cheng 2023 Brief Bioinform 24:bbad035) | Web-friendly; Bayesian incongruence test | Modern eukaryote-friendly | Computationally heavy at genome scale |
| Probabilistic DTL reconciliation | ALE (Szöllősi 2013) | Amalgamated likelihood over gene-tree sample | Bayesian-posterior over D/T/L events; explicit donor inference | Requires gene tree distribution (bootstrap or UFBoot) |
| Probabilistic DTL reconciliation | GeneRax (Morel 2020) | ML reconciliation; species-tree-aware | Faster than ALE; refines noisy gene trees | Less uncertainty quantification than ALE |
| Probabilistic DTL reconciliation | AleRax (Morel 2024) | Co-estimates gene + species trees + DTL rates | Gold standard 2024; corrects gene-tree-error feedback | Computationally heavy; needs >= 20 species |
| Parsimony reconciliation | RANGER-DTL 2.0 (Bansal 2018 Bioinformatics 34:3214) | Min-cost DTL parsimony | Fast; deterministic; many trees | No likelihood; sensitive to event-cost choice |
| Metagenome HGT | MetaCHIP (Song 2019 Microbiome 7:36) | BLAST + phylogeny on MAG-pairs | Designed for metagenome-assembled genomes | Requires high-quality MAGs (>= 90% complete) |
| HGT-aware species tree | ASTRAL-Pro2 (Zhang 2022 Bioinformatics 38:i131) | Quartet-coalescent with paralog handling | Robust to HGT-inflated gene-tree discord | Still assumes ILS-coalescent; not explicit HGT model |

Methodology evolves; verify the current AleRax / AvP documentation and the Szöllősi 2024 review (eLife 13:RP91040) before committing to a single approach. ALE/GeneRax/AleRax have largely superseded older parsimony reconciliation for bacterial phylogenomics.

## Decision Tree by Experimental Scenario

| Scenario | Recommended approach | Why |
|----------|------------------------|-----|
| Single bacterial genome, recent HGT screen | IslandViewer 4 (web) + HGTector v2 | Composition + BLAST distribution; standard 1-genome workflow |
| 5-200 bacterial genomes, ancient HGT focus | ALE or AleRax on orthogroup trees | Probabilistic DTL; recovers ancient transfers obscured by amelioration |
| 200+ bacterial genomes, phylogenomic HGT rates | GeneRax (faster) -> ALE (validation on top candidates) | Scales; ALE only for the candidates needing posterior support |
| Eukaryote genome, suspected HGT | **Contamination check first** (see below); then AvP or HGTphyloDetect | Eukaryote HGT field is dominated by contamination false positives |
| Metagenome / MAG analysis | MetaCHIP (Song 2019) | Designed for MAGs; tolerates fragmentation |
| Gene-family-level HGT rate inference | ALE/AleRax with site-rate variation | Posterior over D/T/L rates; quantitative inference |
| Donor inference (which lineage was the source) | ALE branch-wise D/T/L map; AvP donor placement | Both attach donor branch posterior |
| Plant-plant HGT (parasitic-host) | AvP with broader plant taxa; manual gene-tree inspection | Standard methods often miss plant-plant transfers |
| Putative HGT correlated with antibiotic resistance | IslandViewer + AMRFinderPlus + mobileOG-db | Combine HGT detection with mobile-element + resistance annotation |
| Phage-mediated transfer screen | PHASTER / PhageBoost + IslandViewer | Phage detection orthogonal to general HGT |
| Endosymbiotic gene transfer (organelle -> nucleus) | Custom: BLAST nuclear proteome against mitochondrial/plastid proteome; tree per hit | Standard HGT tools miss EGT context; expect ~5-15% of nuclear plant proteome is plastid-derived |
| Putative HGT shows incongruence but no other evidence | Test against ILS, DGL, hybridization | Phylogenetic discordance has biological alternatives (Maddison 1997 Syst Biol 46:523) |

## Per-Tool Failure Modes

### Contamination masquerading as eukaryotic HGT (THE critical failure)

**Trigger:** Eukaryote genome assembly, especially from non-axenic culture, mi