
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:16 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/chr4_11164.phylip" (19 taxa, 427 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: HKYG


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
GTRG	44	-1140.8864	2380.1393	0.5379	0.5379
GTRI	44	-1141.6969	2381.7603	0.2392	0.7771
GTRIG	45	-1140.6043	2382.0748	0.2044	0.9815
HKYG	40	-1149.8520	2388.2014	0.0096	0.9911
HKYIG	41	-1149.2252	2389.3959	0.0053	0.9963
HKYI	40	-1150.8074	2390.1121	0.0037	1.0000
GTR	43	-1157.7214	2411.3227	0.0000	1.0000
K2PG	37	-1166.7833	2414.7953	0.0000	1.0000
K2PIG	38	-1165.9386	2415.5163	0.0000	1.0000
SYMG	41	-1162.6975	2416.3405	0.0000	1.0000
K2PI	37	-1167.7707	2416.7703	0.0000	1.0000
SYMIG	42	-1162.0587	2417.5237	0.0000	1.0000
HKY	39	-1166.0691	2418.2001	0.0000	1.0000
SYMI	41	-1163.6858	2418.3171	0.0000	1.0000
F81G	39	-1166.5555	2419.1730	0.0000	1.0000
F81IG	40	-1165.9038	2420.3049	0.0000	1.0000
F81I	39	-1167.7963	2421.6545	0.0000	1.0000
JC69G	36	-1182.3307	2443.4921	0.0000	1.0000
JC69IG	37	-1181.5598	2444.3483	0.0000	1.0000
JC69I	36	-1183.3424	2445.5155	0.0000	1.0000
SYM	40	-1179.3864	2447.2702	0.0000	1.0000
K2P	36	-1184.7626	2448.3560	0.0000	1.0000
F81	38	-1182.9242	2449.4875	0.0000	1.0000
JC69	35	-1199.6653	2475.7757	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1140.8864	2369.7728	0.5136	0.5136
GTRIG	45	-1140.6043	2371.2086	0.2505	0.7642
GTRI	44	-1141.6969	2371.3938	0.2284	0.9926
HKYG	40	-1149.8520	2379.7040	0.0036	0.9962
HKYIG	41	-1149.2252	2380.4504	0.0025	0.9986
HKYI	40	-1150.8074	2381.6147	0.0014	1.0000
GTR	43	-1157.7214	2401.4428	0.0000	1.0000
SYMG	41	-1162.6975	2407.3950	0.0000	1.0000
K2PG	37	-1166.7833	2407.5665	0.0000	1.0000
K2PIG	38	-1165.9386	2407.8772	0.0000	1.0000
SYMIG	42	-1162.0587	2408.1175	0.0000	1.0000
SYMI	41	-1163.6858	2409.3716	0.0000	1.0000
K2PI	37	-1167.7707	2409.5415	0.0000	1.0000
HKY	39	-1166.0691	2410.1381	0.0000	1.0000
F81G	39	-1166.5555	2411.1110	0.0000	1.0000
F81IG	40	-1165.9038	2411.8075	0.0000	1.0000
F81I	39	-1167.7963	2413.5925	0.0000	1.0000
JC69G	36	-1182.3307	2436.6614	0.0000	1.0000
JC69IG	37	-1181.5598	2437.1195	0.0000	1.0000
JC69I	36	-1183.3424	2438.6847	0.0000	1.0000
SYM	40	-1179.3864	2438.7728	0.0000	1.0000
K2P	36	-1184.7626	2441.5252	0.0000	1.0000
F81	38	-1182.9242	2441.8483	0.0000	1.0000
JC69	35	-1199.6653	2469.3307	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1149.8520	2541.9754	0.6491	0.6491
HKYI	40	-1150.8074	2543.8861	0.2497	0.8988
HKYIG	41	-1149.2252	2546.7785	0.0588	0.9576
GTRG	44	-1140.8864	2548.2713	0.0279	0.9854
GTRI	44	-1141.6969	2549.8923	0.0124	0.9978
GTRIG	45	-1140.6043	2553.7639	0.0018	0.9996
K2PG	37	-1166.7833	2557.6675	0.0003	0.9999
K2PI	37	-1167.7707	2559.6425	0.0001	1.0000
K2PIG	38	-1165.9386	2562.0350	0.0000	1.0000
HKY	39	-1166.0691	2568.3527	0.0000	1.0000
F81G	39	-1166.5555	2569.3256	0.0000	1.0000
F81I	39	-1167.7963	2571.8071	0.0000	1.0000
SYMG	41	-1162.6975	2573.7232	0.0000	1.0000
F81IG	40	-1165.9038	2574.0789	0.0000	1.0000
SYMI	41	-1163.6858	2575.6997	0.0000	1.0000
GTR	43	-1157.7214	2575.8845	0.0000	1.0000
SYMIG	42	-1162.0587	2578.5024	0.0000	1.0000
JC69G	36	-1182.3307	2582.7056	0.0000	1.0000
JC69I	36	-1183.3424	2584.7290	0.0000	1.0000
JC69IG	37	-1181.5598	2587.2205	0.0000	1.0000
K2P	36	-1184.7626	2587.5694	0.0000	1.0000
F81	38	-1182.9242	2596.0061	0.0000	1.0000
SYM	40	-1179.3864	2601.0442	0.0000	1.0000
JC69	35	-1199.6653	2611.3181	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11164.phylip = 1 - 427;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11164.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11164.phylip = 1 - 427;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11164.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11164.phylip = 1 - 427;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_11164.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;


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End of Output

