Merge branch 'develop' into update_dependencies_pantools

CHANGELOG.md

docs/source/user_guide/msa.rst

docs/source/user_guide/phylogeny.rst

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/MSA.java

...wur/bif/pantools/pangenome/MultipleSequenceAlignment.java

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

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

src/main/resources/Defaults.properties

src/main/resources/MessageBundle.properties

tests/rules/common.smk