Modified the majority vote of the MSA, it seems to work slightly better now. Previously, all characters in a column would be counted and the most common one picked. If it turned out to be a dash, the column would be skipped. This may have given preference to the dashes, and didn't take into account the number of reads which say that there isn't a dash. Now, I'm counting the number of A+C+T+G bases and the number of dashes. If the number of dashes is larger than the sum of bases, the column is skipped, otherwise, the most common base is output.
Modified the majority vote of the MSA, it seems to work slightly better now. Previously, all characters in a column would be counted and the most common one picked. If it turned out to be a dash, the column would be skipped. This may have given preference to the dashes, and didn't take into account the number of reads which say that there isn't a dash. Now, I'm counting the number of A+C+T+G bases and the number of dashes. If the number of dashes is larger than the sum of bases, the column is skipped, otherwise, the most common base is output.

isovic/consise,isovic/racon,isovic/racon,isovic/consise