Comparison of alignment accuracy and increasing sequence length, at low indel frequency values. Selected examples with different input trees. The increase in sequence length did not seem to affect alignment accuracy of the majority of the programs. ProbCons and Mafft L-INS-i were the top performers, followed closely by Muscle, T-Coffee, Mafft FFT-NS-2 and Kalign. Dialign2.2, Dialign-T and Clustal W presented a better accuracy than POA in most of the cases. Scale factor: value by which tree's branch lengths are multiplied, making them uniformly change; c is the Qian-Goldstein distribution value that determines average length of indels.