Time comparison of fastprot vs protdist . This figure shows the time comparison between fastprot and protdist on 10 protein families with family size ranging from 1,000 to 10,000. The time duration for each experiment was limited to 24 hours. We can see that fastprot clearly outperforms protdist when computing distance matrices for protein families. protdist took 14.07 hours to compute the distance matrix for a protein family of size 2,000 while fastprot computed it in 0.16 hours.