Pipeline working from aligned reads (Step 2 and onwards)

.gitignore

src/workflow/Snakefile

src/workflow/default_config.yaml

src/workflow/envs/abpoa.yaml

src/workflow/envs/kalign2.yaml

src/workflow/envs/kalign3.yaml

src/workflow/envs/muscle.yaml

src/workflow/envs/spoa.yaml