Table 3. HomFam benchmarking results
93⩽N⩽2957 (41 families)3127⩽N⩽9105 (33 families)10 099⩽N⩽50 157 (18 families)
AlignerTC/t (s)TC/t (s)TC/t (s)
Clustal Ω0.708/2114.00.639/11 719.50.464/27 328.9
Kalign0.569/324.90.563/6752.00.420/286 711.0
MAFFT default0.550/238.90.462/3115.4−/−
MAFFT –parttree−/−−/−0.253/6119.4
MUSCLE default0.533/104 587.0−/−−/−
MUSCLE –maxiters 2−/−0.416/8239.20.216/110 292.0
  • The columns show total column score (TC) and total run time in seconds for groupings of small (<3000 sequences), medium (3000–10 000 sequences) and large (>10 000 sequences) HomFam test cases.