Merge branch 'release_v4.1.1' into 'pantools_v4'

.gitlab-ci.yml

.idea/vcs.xml

.pre-commit-config.yaml

CHANGELOG.md

README.md

docs/source/_ext/substitutioncodeblock.py

docs/source/conf.py

docs/source/index.rst

docs/source/tables/functional_databases.csv

docs/source/user_guide/construct.rst

docs/source/user_guide/install.rst

docs/source/user_guide/phylogeny.rst

docs/source/user_guide/workflows.rst

pom.xml

...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