.gitignore
.sonarcloud.properties
.travis.yml
CHANGES.md
CONTRIBUTING.md
LICENSE
README.md
THANKS.md
TODO.md
setup.py
alv/__init__.py
alv/alignment.py
alv/alignmentterminal.py
alv/colorize.py
alv/exceptions.py
alv/io.py
alv/version.py
alv.egg-info/PKG-INFO
alv.egg-info/SOURCES.txt
alv.egg-info/dependency_links.txt
alv.egg-info/requires.txt
alv.egg-info/top_level.txt
bin/alv
doc/PF00005_yeast.png
doc/citation.bib
doc/screenshot_1.png
doc/screenshot_2.png
doc/screenshot_PF00005.png
doc/joss/README.txt
doc/joss/paper.bib
doc/joss/paper.md
doc/joss/screenshot.png
tests/PF00005_seed.txt
tests/PF00005_small.fa
tests/PF00005_small.sthlm
tests/PF07690_seed.txt
tests/README.md
tests/__init__.py
tests/cds.fa
tests/long_al.fa
tests/t0.fa
tests/t1.fa
tests/t2.fa
tests/t3.fa
tests/t4.fa
tests/t4.sthlm
tests/t5.fa
tests/t6.fa
tests/t7.fa
tests/t8.fa
tests/t9.fa
tests/test.nex
tests/test_alignment.py
tests/test_io.py
tests/tmem184a_macse_AA.fasta
tests/tmem184a_macse_NT.fasta
tests/woodsia_chloropl_excl_hybrid.fasta