Comparison of alignment accuracy and increasing sequence length, at high indel frequency values. Selected examples obtained with different tree topologies. ProbCons and Mafft L-INS-i took turns as top performers. A middle group of programs is revealed by this comparison, comprising Mafft FFT-NS-2, T-Coffee, Muscle and Kalign. The smallest accuracies were shown by Dialign2.2, Dialign-T and POA, and Clustal W at large sequence sizes. Clustal W curves presented a steep decline in accuracy as the sequence length was increased.