CodonAdaptPy

User guide

  • Getting started
    • Choose an installation
    • Analyze one coding sequence
    • Analyze a file
    • Boundary-aware per-isolate analysis
    • Save reproducible outputs
  • Input and validation guide
    • Metadata
  • Metric definitions and implementation notes
    • Reference-dependent adaptation
    • Intrinsic usage
    • Composition and pairs
    • Host comparison
    • Evolutionary diagnostics
  • Interpretation and known limitations
  • Command-line interface
    • Analyze coding sequences
    • Compare host references
    • Build a reference
    • Infer a phylogeny
    • Optimize a coding sequence

Developer reference

  • Python API and extension guide
    • Phylogenetic and temporal API
    • High-level analysis API
      • AnalysisConfig
      • CodonAnalyzer
        • CodonAnalyzer.analyze()
        • CodonAnalyzer.analyze_many()
        • CodonAnalyzer.analyze_cds_collection()
        • CodonAnalyzer.analyze_file()
      • analyzer_from_reference_files()
    • Sequence models and validation
      • SequenceRecord
        • SequenceRecord.to_dict()
      • ValidationConfig
      • ValidationReport
        • ValidationReport.is_valid
        • ValidationReport.errors
        • ValidationReport.warnings
        • ValidationReport.to_dict()
      • SequenceValidator
        • SequenceValidator.validate()
      • SequenceParser
        • SequenceParser.parse()
        • SequenceParser.parse_fasta()
        • SequenceParser.parse_table()
        • SequenceParser.parse_genbank()
        • SequenceParser.attach_metadata()
        • SequenceParser.parse_zip()
    • References and aggregation
      • ReferenceProfile
        • ReferenceProfile.to_dict()
      • ReferenceManager
        • ReferenceManager.register()
        • ReferenceManager.from_sequences()
        • ReferenceManager.get()
        • ReferenceManager.list()
        • ReferenceManager.save()
        • ReferenceManager.load()
      • CDSAggregator
        • CDSAggregator.analyze()
      • IsolateAnalysis
        • IsolateAnalysis.to_dict()
    • Comparative analysis and visualization
      • ComparativeAnalyzer
        • ComparativeAnalyzer.summarize()
        • ComparativeAnalyzer.group_summaries()
        • ComparativeAnalyzer.compare_two_groups()
        • ComparativeAnalyzer.automatic_test()
        • ComparativeAnalyzer.adjust_bh()
        • ComparativeAnalyzer.multivariate()
        • ComparativeAnalyzer.hierarchical_clustering()
        • ComparativeAnalyzer.linear_discriminant()
        • ComparativeAnalyzer.repeated_grouped_discriminant()
        • ComparativeAnalyzer.correspondence_analysis()
      • PlotManager
        • PlotManager.rscu_heatmap()
        • PlotManager.enc_gc3()
        • PlotManager.sliding_cai()
        • PlotManager.neutrality()
        • PlotManager.parity_rule_2()
        • PlotManager.save()
      • PublicationPlotManager
        • PublicationPlotManager.ordination()
        • PublicationPlotManager.metric_panels()
        • PublicationPlotManager.codon_preference_intersections()
        • PublicationPlotManager.codon_preference_upset()
        • PublicationPlotManager.rscu_similarity_heatmap()
        • PublicationPlotManager.rscu_pca_biplot()
        • PublicationPlotManager.sliding_cai()
        • PublicationPlotManager.metric_correlation_heatmap()
        • PublicationPlotManager.host_adaptation_landscape()
        • PublicationPlotManager.dinucleotide_heatmap()
        • PublicationPlotManager.rscu_heatmap()
        • PublicationPlotManager.evolutionary_diagnostics()
        • PublicationPlotManager.rscu_profiles()
        • PublicationPlotManager.dinucleotide_profiles()
        • PublicationPlotManager.composition_overview()
        • PublicationPlotManager.lda_evaluation()
        • PublicationPlotManager.host_adaptation()
        • PublicationPlotManager.bland_altman_validation()
        • PublicationPlotManager.repeated_cv_distribution()
        • PublicationPlotManager.save()
    • Phylogenetics and temporal analysis
      • PhylogeneticAnalyzer
        • PhylogeneticAnalyzer.write_fasta()
        • PhylogeneticAnalyzer.align()
        • PhylogeneticAnalyzer.trim()
        • PhylogeneticAnalyzer.infer_tree()
        • PhylogeneticAnalyzer.run()
      • TemporalAnalyzer
        • TemporalAnalyzer.load_tree()
        • TemporalAnalyzer.temporal_signal()
        • TemporalAnalyzer.date_tree()
        • TemporalAnalyzer.lineage_through_time()
      • PhylogeneticComparator
        • PhylogeneticComparator.robinson_foulds()
      • ETE3TreePlotter
        • ETE3TreePlotter.tree()
        • ETE3TreePlotter.temporal_signal()
        • ETE3TreePlotter.lineage_through_time()
        • ETE3TreePlotter.save()
    • Sequence design and reporting
      • OptimizationConfig
      • CodonOptimizer
        • CodonOptimizer.optimize()
      • ReportGenerator
        • ReportGenerator.write_json()
        • ReportGenerator.write_table()
        • ReportGenerator.write_html()
        • ReportGenerator.write_excel()
        • ReportGenerator.write_pdf()
        • ReportGenerator.write_optimized_fasta()
CodonAdaptPy
  • Search

© Copyright 2026, Naveen Duhan.

Built with Sphinx using a theme provided by Read the Docs.