input sequence file

Preset Mode quickaln

Distance matrix computation method slowfastvery fastktupaln

Tree Computation method gotoh pair-wisemyers-miller pair-wisefasta pair-wisecfasta pair-wise

Number of diagonals used by the fasta_pair_wise algorithm

Number of diagonals used by the fasta pair-wise algorithm 01

Diagonal threshold

Alphabet degeneration method vasilikyidmat

Substitution Matrix blosum62mt

Match penalty

Gap opening penalty

Gap extension penalty

Cosmetic penalty

Terminal gaps penalty 012

Number of iterations

Output order inputaligned

Input order inputaligned