
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:51 02/24/2011

Input data from file "/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23160.phylip" (19 taxa, 180 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: K2PI


Note: number of parameters compared to sample size
is low (Nchar/Nparams < 40). Consider the use of AICc.


(Output sorted by AICc. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AICc		wAICc	cwAICc
HKYI	40	-523.0438	1149.6848	0.4676	0.4676
HKYG	40	-523.4363	1150.4698	0.3158	0.7835
K2PI	37	-529.8313	1153.4653	0.0706	0.8541
HKYIG	41	-523.4361	1153.8286	0.0589	0.9130
K2PG	37	-530.1971	1154.1969	0.0490	0.9620
HKY	39	-528.4979	1157.2816	0.0105	0.9725
K2PIG	38	-530.1968	1157.4148	0.0098	0.9823
F81I	39	-529.0323	1158.3503	0.0061	0.9884
F81G	39	-529.4266	1159.1389	0.0041	0.9925
GTRI	44	-521.7932	1160.9197	0.0017	0.9942
JC69I	36	-535.3845	1161.3983	0.0013	0.9956
GTRG	44	-522.1387	1161.6107	0.0012	0.9968
JC69G	36	-535.7703	1162.1699	0.0009	0.9977
F81IG	40	-529.4263	1162.4497	0.0008	0.9985
K2P	36	-536.1581	1162.9455	0.0006	0.9991
GTRIG	45	-522.2010	1165.2975	0.0002	0.9993
JC69IG	37	-535.7700	1165.3428	0.0002	0.9995
SYMI	41	-529.3462	1165.6489	0.0002	0.9996
F81	38	-534.5234	1166.0680	0.0001	0.9998
SYMG	41	-529.7212	1166.3989	0.0001	0.9999
GTR	43	-526.5207	1166.8650	0.0001	1.0000
SYMIG	42	-529.7209	1169.8068	0.0000	1.0000
JC69	35	-541.4974	1170.4949	0.0000	1.0000
SYM	40	-535.4607	1174.5186	0.0000	1.0000



(Output sorted by AIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-523.0438	1126.0877	0.4714	0.4714
HKYG	40	-523.4363	1126.8726	0.3184	0.7898
HKYIG	41	-523.4361	1128.8721	0.1172	0.9070
GTRI	44	-521.7932	1131.5864	0.0302	0.9372
GTRG	44	-522.1387	1132.2774	0.0213	0.9585
K2PI	37	-529.8313	1133.6625	0.0107	0.9692
K2PG	37	-530.1971	1134.3941	0.0074	0.9766
GTRIG	45	-522.2010	1134.4020	0.0074	0.9840
HKY	39	-528.4979	1134.9959	0.0055	0.9894
F81I	39	-529.0323	1136.0646	0.0032	0.9927
K2PIG	38	-530.1968	1136.3935	0.0027	0.9954
F81G	39	-529.4266	1136.8532	0.0022	0.9976
F81IG	40	-529.4263	1138.8526	0.0008	0.9984
GTR	43	-526.5207	1139.0415	0.0007	0.9991
SYMI	41	-529.3462	1140.6923	0.0003	0.9994
SYMG	41	-529.7212	1141.4424	0.0002	0.9996
JC69I	36	-535.3845	1142.7690	0.0001	0.9997
SYMIG	42	-529.7209	1143.4418	0.0001	0.9998
JC69G	36	-535.7703	1143.5405	0.0001	0.9999
K2P	36	-536.1581	1144.3161	0.0001	0.9999
F81	38	-534.5234	1145.0468	0.0000	1.0000
JC69IG	37	-535.7700	1145.5399	0.0000	1.0000
SYM	40	-535.4607	1150.9215	0.0000	1.0000
JC69	35	-541.4974	1152.9949	0.0000	1.0000



(Output sorted by BIC. w: Akaike weight, cw: cumulative w.)

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-529.8313	1251.8019	0.3941	0.3941
K2PG	37	-530.1971	1252.5335	0.2733	0.6674
HKYI	40	-523.0438	1253.8059	0.1447	0.8121
HKYG	40	-523.4363	1254.5909	0.0977	0.9098
JC69I	36	-535.3845	1257.7154	0.0205	0.9303
K2PIG	38	-530.1968	1257.7259	0.0204	0.9507
JC69G	36	-535.7703	1258.4869	0.0139	0.9646
K2P	36	-536.1581	1259.2626	0.0095	0.9740
HKY	39	-528.4979	1259.5212	0.0083	0.9823
HKYIG	41	-523.4361	1259.7833	0.0073	0.9896
F81I	39	-529.0323	1260.5899	0.0049	0.9945
F81G	39	-529.4266	1261.3785	0.0033	0.9978
JC69IG	37	-535.7700	1263.6793	0.0010	0.9988
JC69	35	-541.4974	1264.7484	0.0006	0.9994
F81	38	-534.5234	1266.3791	0.0003	0.9997
F81IG	40	-529.4263	1266.5709	0.0002	0.9999
SYMI	41	-529.3462	1271.6036	0.0000	1.0000
GTRI	44	-521.7932	1272.0765	0.0000	1.0000
SYMG	41	-529.7212	1272.3536	0.0000	1.0000
GTRG	44	-522.1387	1272.7675	0.0000	1.0000
GTR	43	-526.5207	1276.3386	0.0000	1.0000
SYMIG	42	-529.7209	1277.5460	0.0000	1.0000
GTRIG	45	-522.2010	1278.0850	0.0000	1.0000
SYM	40	-535.4607	1278.6398	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23160.phylip = 1 - 180;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23160.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23160.phylip = 1 - 180;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23160.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23160.phylip = 1 - 180;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23160.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

