├── .gitignore ├── LICENSE ├── README.md ├── SDDetector ├── Db │ ├── AlignDB.py │ ├── GeneDB.py │ ├── SqliteDB.py │ └── __init__.py ├── Entities │ ├── Alignment.py │ ├── CDS.py │ ├── Chain.py │ ├── Duplication.py │ ├── Feature.py │ ├── Gene.py │ ├── GeneLink.py │ ├── Region.py │ ├── Transcript.py │ └── __init__.py ├── Parser │ ├── Blast │ │ ├── BlastTabParser.py │ │ ├── BlastXMLParser.py │ │ ├── BlastXMLParserExpat.py │ │ └── __init__.py │ ├── Gff │ │ ├── GffDuplicationParser.py │ │ ├── GffGeneParser.py │ │ ├── GffTEParser.py │ │ └── __init__.py │ └── __init__.py ├── Utils │ ├── AlignmentChainer.py │ ├── CircosPlot.py │ ├── EffectPredictor.py │ ├── FastaFileIndexer.py │ └── __init__.py ├── __init__.py └── version.py ├── bin ├── segmental_duplication_detector.py ├── segmental_duplication_filter.py └── segmental_duplication_gene_analyzer.py ├── data ├── arabido.tar.gz └── colleto.tar.gz ├── images ├── arabido.png ├── colleto.png └── colleto_refined.png ├── requirements.txt ├── setup.py ├── test-data ├── README ├── TE.gff3 ├── TE.txt ├── blast.tab ├── blast.xml ├── circos.conf ├── circos2.conf ├── circos3.conf ├── gene-link.txt ├── gene.gff3 ├── gene.txt ├── genome.txt ├── sdd.gff3 ├── segdup.txt ├── seq.fasta ├── seq.nhr ├── seq.nin ├── seq.nog ├── seq.nsd ├── seq.nsi ├── seq.nsq └── similarity.txt └── tests ├── __init__.py ├── test_AlignDB.py ├── test_AlignmentChainer.py ├── test_BlastTabParser.py ├── test_BlastXMLParser.py ├── test_BlastXMLParserExpat.py ├── test_CircosPlot.py ├── test_Duplication.py ├── test_EffectPredictor.py ├── test_FastaFileIndexer.py ├── test_GeneDB.py ├── test_GeneLink.py ├── test_GffDuplicationParser.py ├── test_GffGeneParser.py └── test_GffTEParser.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nlapalu/SDDetector/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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