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Table 6 Real Dataset Analysis. Results of the model selection on the specialised datasets (see the references for full descriptions of the individual datasets). Amino acid matrix expectations are based on previously published information about the sequences ([19, 54, 55] and LANL [56]).

From: Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

Dataset Source Expected AIC1 AIC2 BIC
mtCDNApri Yang [54] MtMam MtMam+I+G MtMam+G MtMam+G
mtCDNAape Yang [54] MtMam MtMam+F MtMam+F MtMam+F
70pep_nogap Reyes et al. [55] MtMam MtMam+I+G+F MtMam+I+G MtMam+I+G
BETA Dimmic et al. [19] RtREV RtREV+G+F RtREV+G RtREV+G
ENDO Dimmic et al. [19] RtREV RtREV+I+G+F RtREV+I+G+F RtREV+I+G+F
GAGGAM Dimmic et al. [19] JTT JTT+G+F JTT+G+F JTT+G+F
GAGHIV Dimmic et al. [19] JTT JTT+G+F JTT+G+F JTT+G+F
GAMMA Dimmic et al. [19] RtREV CPREV+G+F RtREV+G RtREV+G
LENTI Dimmic et al. [19] RtREV RtREV+I+G+F RtREV+I+G+F RtREV+I+G+F
SPUMA Dimmic et al. [19] RtREV RtREV+G RtREV+G RtREV+G
NONLTR Dimmic et al. [19] RtREV RtREV+I+G+F RtREV+I+G+F RtREV+I+G+F
SIVPOLPRO LANL RtREV RtREV+G+F RtREV+G+F RtREV+G