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Ray
@iminkin Let me show you the example.  In this screeshot, there is a negative block ("-") of HCV_527. In fact, the original sequence of HCV_527 should be the reverse...
Ok. These 2 sequences are uploaded. :) [HCV.zip](https://github.com/medvedevgroup/SibeliaZ/files/5006790/HCV.zip)
The command-line I used to generate the alignment with SibeliaZ: `sibeliaz -t 6 -k 15 HCV_mutation_strain_new.fasta` The command-line I used to convert MSA to GFA: `python maf_to_gfa1.py sibeliaz_out/alignment.maf HCV_mutation_strain_new.fasta >...
Ok. Thanks! Finally, I used this email address: [email protected]. You can check it.