storing scoring matrices as resource files

CHANGELOG.md

docs/source/user_guide/construct.rst

docs/source/user_guide/phylogeny.rst

...bif/pantools/alignment/BoundedLocalSequenceAlignment.java

...nl/wur/bif/pantools/alignment/LocalSequenceAlignment.java

src/main/java/nl/wur/bif/pantools/cli/AddFunctions.java

src/main/java/nl/wur/bif/pantools/cli/ConsensusTree.java

src/main/java/nl/wur/bif/pantools/cli/CorePhylogeny.java

src/main/java/nl/wur/bif/pantools/cli/Group.java

src/main/java/nl/wur/bif/pantools/cli/MSA.java

src/main/java/nl/wur/bif/pantools/cli/OptimalGrouping.java

.../java/nl/wur/bif/pantools/cli/validation/Constraints.java

...ols/cli/validation/validators/ScoringMatrixValidator.java

...in/java/nl/wur/bif/pantools/pangenome/Classification.java

src/main/java/nl/wur/bif/pantools/pangenome/GenomeLayer.java

src/main/java/nl/wur/bif/pantools/pangenome/Phylogeny.java

...ain/java/nl/wur/bif/pantools/pangenome/ProteomeLayer.java

src/main/java/nl/wur/bif/pantools/utils/FileUtils.java

src/main/java/nl/wur/bif/pantools/utils/Globals.java

src/main/resources/Defaults.properties