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Merge remote-tracking branch 'refs/remotes/origin/phased_pangenomics' into phased_pangenomics
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- CHANGELOG.md 1 addition, 1 deletionCHANGELOG.md
- docs/source/user_guide/construct.rst 11 additions, 12 deletionsdocs/source/user_guide/construct.rst
- src/main/java/nl/wur/bif/pantools/analysis/blast/Blast.java 8 additions, 120 deletionssrc/main/java/nl/wur/bif/pantools/analysis/blast/Blast.java
- src/main/java/nl/wur/bif/pantools/analysis/blast/BlastCLI.java 0 additions, 3 deletions...ain/java/nl/wur/bif/pantools/analysis/blast/BlastCLI.java
- src/main/java/nl/wur/bif/pantools/analysis/calculate_dn_ds/CalculateDnDs.java 0 additions, 1 deletion.../bif/pantools/analysis/calculate_dn_ds/CalculateDnDs.java
- src/main/java/nl/wur/bif/pantools/analysis/calculate_dn_ds/NeedlemanWunschAlign.java 0 additions, 46 deletions...ntools/analysis/calculate_dn_ds/NeedlemanWunschAlign.java
- src/main/java/nl/wur/bif/pantools/analysis/classification/Classification.java 0 additions, 14 deletions.../bif/pantools/analysis/classification/Classification.java
- src/main/java/nl/wur/bif/pantools/analysis/gene_retention/GeneRetention.java 0 additions, 57 deletions...r/bif/pantools/analysis/gene_retention/GeneRetention.java
- src/main/java/nl/wur/bif/pantools/analysis/kmer_classification/KmerClassification.java 0 additions, 1 deletion...ools/analysis/kmer_classification/KmerClassification.java
- src/main/java/nl/wur/bif/pantools/analysis/phylogeny/create_tree_template/CreateTreeTemplate.java 0 additions, 33 deletions...is/phylogeny/create_tree_template/CreateTreeTemplate.java
- src/main/java/nl/wur/bif/pantools/construction/annotations/AnnotationLayer.java 0 additions, 48 deletions...if/pantools/construction/annotations/AnnotationLayer.java
- src/main/java/nl/wur/bif/pantools/construction/phasing/AddPhasing.java 0 additions, 173 deletions.../nl/wur/bif/pantools/construction/phasing/AddPhasing.java
- src/main/java/nl/wur/bif/pantools/construction/synteny/Synteny.java 0 additions, 139 deletions...ava/nl/wur/bif/pantools/construction/synteny/Synteny.java
- src/main/java/nl/wur/bif/pantools/utils/Utils.java 16 additions, 3 deletionssrc/main/java/nl/wur/bif/pantools/utils/Utils.java
- src/main/resources/MessageBundle.properties 1 addition, 1 deletionsrc/main/resources/MessageBundle.properties
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