Skip to main content

Table 1 The quality of constructed multiple sequence alignment (MSA) with the algorithms based on the sum-of-pair score (SP-score), the column score (C-score), and the Transitive Consistency Score (TCS-score), and the predicted best amino acid substitution model based on the lowest BICa score (A) and the calculated maximum log-likelihood for constructed tree from each MSA set (B)

From: Comparative phylogeny and evolutionary analysis of Dicer-like protein family in two plant monophyletic lineages

Alignment algorithm Liliopsida lineage Eudicotyledons lineage
SP-score TC-score TCS-score A BIC* scores B** SP-score TC-score TCS-score A BIC scores B
T-coffee 326748 108 891 JTT + G + I + F*** 61968.7167205287 − 30581.59 17432842 5 883 JTT + G 31409.2078965051 − 13324.74
MUSCLE 328078 101 881 JTT + G + I + F 61542.366184322 − 30401.81 17489758 11 866 JTT + G 31230.133303795 − 13347.87
Kalign 327823 133 875 JTT + G + I + F 63956.652705501 − 31582.69 17301996 5 836 JTT + G 40832.5711781908 − 18038.05
Clustal omega 324620 110 855 JTT + G + I + F 62178.742941649 − 30694.67 17217684 7 854 JTT + G 32693.3283402443 − 14250.52
MAFT 328316 112 885 JTT + G + I + F 62421.8477405952 − 30804.25 17619344 13 883 JTT + G 33692.6193749731 − 14453.60
  1. ***JTT Jones-Taylor-Thornton, G discrete Gamma distribution, I a certain fraction of sites is evolutionarily invariable, F amino acid frequencies
  2. **The tree was inferred by Neighbor-Joining method
  3. *BIC Bayesian Information Criterion