
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:54 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/chr5_5183.phylip" (19 taxa, 186 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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
HKYG	40	-463.1402	1028.9011	0.4000	0.4000
HKYI	40	-463.1554	1028.9315	0.3939	0.7939
HKYIG	41	-462.8385	1031.5937	0.1041	0.8980
K2PG	37	-470.4539	1033.9078	0.0327	0.9307
K2PI	37	-470.5307	1034.0614	0.0303	0.9611
K2PIG	38	-470.1733	1036.5098	0.0089	0.9700
GTRG	44	-460.2187	1036.5225	0.0089	0.9788
GTRI	44	-460.2521	1036.5893	0.0086	0.9874
SYMG	41	-465.9211	1037.7589	0.0048	0.9921
SYMI	41	-465.9913	1037.8992	0.0044	0.9966
GTRIG	45	-459.9455	1039.4625	0.0020	0.9986
SYMIG	42	-465.6931	1040.6449	0.0011	0.9998
HKY	39	-472.5773	1044.5245	0.0002	0.9999
K2P	36	-478.7621	1047.4034	0.0000	1.0000
GTR	43	-468.7323	1050.1124	0.0000	1.0000
SYM	40	-473.7755	1050.1717	0.0000	1.0000
F81G	39	-475.6878	1050.7454	0.0000	1.0000
F81I	39	-475.7328	1050.8356	0.0000	1.0000
JC69G	36	-481.5906	1053.0604	0.0000	1.0000
JC69I	36	-481.6482	1053.1756	0.0000	1.0000
F81IG	40	-475.4598	1053.5402	0.0000	1.0000
JC69IG	37	-481.4025	1055.8050	0.0000	1.0000
F81	38	-484.3421	1064.8474	0.0000	1.0000
JC69	35	-489.9018	1066.6036	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-463.1402	1006.2804	0.2939	0.2939
HKYI	40	-463.1554	1006.3109	0.2894	0.5833
HKYIG	41	-462.8385	1007.6770	0.1462	0.7294
GTRG	44	-460.2187	1008.4374	0.0999	0.8294
GTRI	44	-460.2521	1008.5042	0.0967	0.9260
GTRIG	45	-459.9455	1009.8910	0.0483	0.9743
SYMG	41	-465.9211	1013.8423	0.0067	0.9810
SYMI	41	-465.9913	1013.9825	0.0062	0.9873
K2PG	37	-470.4539	1014.9078	0.0039	0.9912
K2PI	37	-470.5307	1015.0614	0.0036	0.9949
SYMIG	42	-465.6931	1015.3862	0.0031	0.9979
K2PIG	38	-470.1733	1016.3466	0.0019	0.9999
HKY	39	-472.5773	1023.1546	0.0001	0.9999
GTR	43	-468.7323	1023.4645	0.0001	1.0000
SYM	40	-473.7755	1027.5510	0.0000	1.0000
F81G	39	-475.6878	1029.3755	0.0000	1.0000
F81I	39	-475.7328	1029.4657	0.0000	1.0000
K2P	36	-478.7621	1029.5242	0.0000	1.0000
F81IG	40	-475.4598	1030.9195	0.0000	1.0000
JC69G	36	-481.5906	1035.1812	0.0000	1.0000
JC69I	36	-481.6482	1035.2964	0.0000	1.0000
JC69IG	37	-481.4025	1036.8050	0.0000	1.0000
F81	38	-484.3421	1044.6841	0.0000	1.0000
JC69	35	-489.9018	1049.8036	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-470.4539	1134.2604	0.3061	0.3061
K2PI	37	-470.5307	1134.4140	0.2835	0.5896
HKYG	40	-463.1402	1135.3102	0.1811	0.7707
HKYI	40	-463.1554	1135.3407	0.1784	0.9491
K2PIG	38	-470.1733	1138.9249	0.0297	0.9788
HKYIG	41	-462.8385	1139.9326	0.0180	0.9968
K2P	36	-478.7621	1145.6511	0.0010	0.9978
SYMG	41	-465.9211	1146.0979	0.0008	0.9986
SYMI	41	-465.9913	1146.2382	0.0008	0.9994
HKY	39	-472.5773	1148.9588	0.0002	0.9996
GTRG	44	-460.2187	1150.3703	0.0001	0.9997
GTRI	44	-460.2521	1150.4371	0.0001	0.9998
SYMIG	42	-465.6931	1150.8676	0.0001	0.9998
JC69G	36	-481.5906	1151.3081	0.0001	0.9999
JC69I	36	-481.6482	1151.4233	0.0001	1.0000
GTRIG	45	-459.9455	1155.0496	0.0000	1.0000
F81G	39	-475.6878	1155.1796	0.0000	1.0000
F81I	39	-475.7328	1155.2698	0.0000	1.0000
JC69IG	37	-481.4025	1156.1576	0.0000	1.0000
SYM	40	-473.7755	1156.5809	0.0000	1.0000
F81IG	40	-475.4598	1159.9494	0.0000	1.0000
GTR	43	-468.7323	1162.1716	0.0000	1.0000
JC69	35	-489.9018	1162.7048	0.0000	1.0000
F81	38	-484.3421	1167.2625	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_5183.phylip = 1 - 186;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_5183.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_5183.phylip = 1 - 186;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_5183.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_5183.phylip = 1 - 186;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_5183.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

