Merge branch 'release_v4.1.0' into 'pantools_v4'

.gitignore

.gitlab-ci.yml

.idea/inspectionProfiles/Project_Default.xml

.idea/misc.xml

.pre-commit-config.yaml

CHANGELOG.md

docs/source/conf.py

docs/source/index.rst

docs/source/tutorial/tutorial_part1.rst

docs/source/tutorial/tutorial_part2.rst

docs/source/tutorial/tutorial_part3.rst

docs/source/tutorial/tutorial_part4.rst

docs/source/tutorial/tutorial_part5.rst

docs/source/user_guide/characterize.rst

docs/source/user_guide/construct.rst

docs/source/user_guide/explore.rst

docs/source/user_guide/install.rst

docs/source/user_guide/mapping.rst

docs/source/user_guide/msa.rst

docs/source/user_guide/phylogeny.rst