Input file

Output sequences order input orderreorder

Sequence type nucleotideamino acidauto

Pairwise alignment computation method fastagenaflocalglobal

FFT approximation fftno fft

Part tree parttreedpparttreefastaparttree

Max iteration number

Partsize

Group size

Guide tree rebuild

Gap opening penalty

Group-to-group gap extension penalty

Gap opening penalty at local pairwise alignment

Matrix blosum100blosum30blosum35blosum40blosum45blosum50blosum55blosum60blosum62blosum65blosum70blosum75blosum80blosum85blosum90blosumndayhoffgonnetidentitymatchpam10pam100pam110pam120pam130pam140pam150pam160pam170pam180pam190pam20pam200pam210pam220pam230pam240pam250pam260pam270pam280pam290pam30pam300pam310pam320pam330pam340pam350pam360pam370pam380pam390pam40pam400pam410pam420pam430pam440pam450pam460pam470pam480pam490pam50pam500pam60pam70pam80pam90