How twilightsail/conservatory works
Conservatory identifies conserved non-coding sequences across related and distant genomes. Users prepare genome data, a genome database, family trees, and neutral models; they then build databases for a reference and run conservation per gene. The documented analysis uses regulatory-sequence alignments and orthology to reconstruct ancestral CNS sequences and search syntenic regions. Results can be merged within a reference and across references. The README describes these capabilities, but no source excerpts were supplied, so internal call wiring beyond documented commands is not inferred.
Main entry points: buildConservation Build conservation · processGenomes Process genomes · mergeCNS Merge CNS · genomes Family trees
Components 16
Reference data
- Genome files
genomes - Genome catalog
genome_database.csv - Family trees
genomes - Neutral models
genomes
Genome preparation
- Process genomes
processGenomes - Orthology database
scripts/buildOrthologDB - Regulatory sequence DB
scripts/buildRegulatorySeqDB
CNS analysis
- Build conservation
scripts/buildConservation - Family alignments
alignments - Synteny mapping
scripts/Mapping.pm - Tree and model
scripts/buildModel - Ancestral reconstruction
scripts/reconstructCNSSequences
CNS results
- Per-gene CNS
CNS - Merge CNS
scripts/mergeCNS - Multi-reference consensus
scripts/mergeCNS
Other components
- Researcher
Connections 18
- Researcher → Process genomes: runs setup
- Genome files → Process genomes: provides genomes
- Genome catalog → Process genomes: configures genomes
- Process genomes → Orthology database: builds orthology
- Process genomes → Regulatory sequence DB: builds sequence DB
- Researcher → Build conservation: runs per gene
- Orthology database → Build conservation: supplies orthology
- Regulatory sequence DB → Build conservation: supplies sequences
- Family trees → Tree and model: provides tree
- Neutral models → Build conservation: sets conservation model
- Family trees → Build conservation: guides comparisons
- Build conservation → Family alignments: produces alignments
- Build conservation → Synteny mapping: uses synteny mapping
- Build conservation → Ancestral reconstruction: reconstructs CNS
- Ancestral reconstruction → Per-gene CNS: writes CNS
- Researcher → Merge CNS: requests merge
- Per-gene CNS → Merge CNS: provides per-gene CNS
- Merge CNS → Multi-reference consensus: combines references