I added the appropriate warnings when options that are not correct for the current mode are selected.
The "Already aligned" option should work as expected in both modes.
Fasta support has been added.
Implementing printing of alignments in the "reference comparison" mode will take more time.
I added the appropriate warnings when options that are not correct for the current mode are selected. The "Already aligned" option should work as expected in both modes. Fasta support has been added.
Implementing printing of alignments in the "reference comparison" mode will take more time.
Closes #57. Closes #56. Closes #55.