Journal of Genetic Engineering and Biotechnology

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 BIC^a 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
Alignment algorithm	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

***JTT Jones-Taylor-Thornton, G discrete Gamma distribution, I a certain fraction of sites is evolutionarily invariable, F amino acid frequencies
**The tree was inferred by Neighbor-Joining method
*BIC Bayesian Information Criterion

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