How moshi4/fastdtlmapper works
FastDTLmapper is a genome-wide gene gain/loss mapper: it takes protein CDS files and a rooted species tree, infers ortholog groups and gene trees, reconciles those trees for DTL events, then aggregates and maps events onto the species tree. The README documents this stage order and optional gain/loss plotting and GO enrichment analysis. The main workflow implementation was not sampled, so the graph shows documented sequencing without attributing unverified calls to particular internal functions.
Main entry points: FastDTLmapper.py Workflow CLI · input_check.py Input validation · __main__.py Orthogroup inference · AnGST_wrapper.py AnGST wrapper
Components 17
Main workflow
- Workflow CLI
src/fastdtlmapper/scripts/FastDTLmapper.py - Input validation
src/fastdtlmapper/input_check.py
Gene tree inference
- Orthogroup inference
src/fastdtlmapper/bin/OrthoFinder/scripts_of/__main__.py - Sequence alignment
- Alignment trimming
- Gene tree reconstruction
- Tree correction
DTL mapping
- AnGST wrapper
src/fastdtlmapper/bin/AnGST_wrapper.py - DTL reconciliation
src/fastdtlmapper/bin/angst/angst_lib/reconcile.py - Event aggregation
src/fastdtlmapper/angst/event_map.py - Mapped tree output
src/fastdtlmapper/util/tree.py
Further analysis
- Gain/loss plotting
src/fastdtlmapper/scripts/plot_gain_loss_map.py - GOEA command
src/fastdtlmapper/scripts/FastDTLgoea.py - GO enrichment
src/fastdtlmapper/goea/goea.py - Orthogroup GO associations
src/fastdtlmapper/goea/og_go_association.py
Other components
- Researcher
- Genome and tree inputs
Connections 16
- Researcher → Genome and tree inputs: provides
- Genome and tree inputs → Workflow CLI: supplies
- Workflow CLI → Input validation: checks inputs
- Input validation → Orthogroup inference: starts analysis
- Orthogroup inference → Sequence alignment: orthogroups
- Sequence alignment → Alignment trimming: alignments
- Alignment trimming → Gene tree reconstruction: trimmed alignments
- Gene tree reconstruction → Tree correction: gene trees
- Tree correction → AnGST wrapper: corrected trees
- AnGST wrapper → DTL reconciliation: runs reconciliation
- DTL reconciliation → Event aggregation: event results
- Event aggregation → Mapped tree output: writes mapped events
- Mapped tree output → Gain/loss plotting: mapped tree
- Researcher → GOEA command: requests enrichment
- GOEA command → GO enrichment: runs analysis
- Orthogroup GO associations → GO enrichment: association data