
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:02 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/chr8_492.phylip" (19 taxa, 351 characters)

Minimum AIC  model: HKYG
Minimum AICc model: K2PG
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
K2PG	37	-1253.9611	2590.9063	0.4189	0.4189
HKYG	40	-1250.7784	2592.1375	0.2263	0.6452
K2PIG	38	-1253.7847	2593.0694	0.1420	0.7873
K2PI	37	-1255.4626	2593.9091	0.0933	0.8806
HKYIG	41	-1250.6302	2594.4060	0.0728	0.9534
HKYI	40	-1252.5657	2595.7119	0.0379	0.9913
SYMG	41	-1253.5095	2600.1645	0.0041	0.9954
GTRG	44	-1250.6425	2602.2262	0.0015	0.9968
SYMIG	42	-1253.3149	2602.3571	0.0014	0.9982
SYMI	41	-1254.8880	2602.9216	0.0010	0.9992
GTRIG	45	-1250.4911	2604.5561	0.0005	0.9997
GTRI	44	-1252.2027	2605.3466	0.0003	1.0000
K2P	36	-1274.3959	2629.2758	0.0000	1.0000
HKY	39	-1270.9654	2629.9630	0.0000	1.0000
SYM	40	-1274.0990	2638.7787	0.0000	1.0000
GTR	43	-1270.6416	2639.6090	0.0000	1.0000
JC69G	36	-1283.7636	2648.0112	0.0000	1.0000
JC69I	36	-1283.9946	2648.4733	0.0000	1.0000
F81G	39	-1281.1068	2650.2457	0.0000	1.0000
JC69IG	37	-1283.6870	2650.3580	0.0000	1.0000
F81I	39	-1281.3493	2650.7308	0.0000	1.0000
F81IG	40	-1281.0453	2652.6712	0.0000	1.0000
JC69	35	-1302.2615	2682.5230	0.0000	1.0000
F81	38	-1299.3313	2684.1625	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1250.7784	2581.5568	0.3275	0.3275
K2PG	37	-1253.9611	2581.9223	0.2728	0.6003
HKYIG	41	-1250.6302	2583.2603	0.1397	0.7401
K2PIG	38	-1253.7847	2583.5694	0.1197	0.8598
K2PI	37	-1255.4626	2584.9251	0.0608	0.9206
HKYI	40	-1252.5657	2585.1313	0.0548	0.9754
SYMG	41	-1253.5095	2589.0189	0.0078	0.9833
GTRG	44	-1250.6425	2589.2850	0.0069	0.9901
SYMIG	42	-1253.3149	2590.6298	0.0035	0.9936
GTRIG	45	-1250.4911	2590.9823	0.0029	0.9966
SYMI	41	-1254.8880	2591.7760	0.0020	0.9986
GTRI	44	-1252.2027	2592.4054	0.0014	1.0000
HKY	39	-1270.9654	2619.9309	0.0000	1.0000
K2P	36	-1274.3959	2620.7917	0.0000	1.0000
GTR	43	-1270.6416	2627.2833	0.0000	1.0000
SYM	40	-1274.0990	2628.1981	0.0000	1.0000
JC69G	36	-1283.7636	2639.5271	0.0000	1.0000
JC69I	36	-1283.9946	2639.9892	0.0000	1.0000
F81G	39	-1281.1068	2640.2135	0.0000	1.0000
F81I	39	-1281.3493	2640.6987	0.0000	1.0000
JC69IG	37	-1283.6870	2641.3740	0.0000	1.0000
F81IG	40	-1281.0453	2642.0906	0.0000	1.0000
JC69	35	-1302.2615	2674.5230	0.0000	1.0000
F81	38	-1299.3313	2674.6625	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1253.9611	2724.7714	0.7746	0.7746
K2PI	37	-1255.4626	2727.7742	0.1726	0.9472
K2PIG	38	-1253.7847	2730.2792	0.0493	0.9965
HKYG	40	-1250.7784	2735.9883	0.0028	0.9993
HKYI	40	-1252.5657	2739.5627	0.0005	0.9998
HKYIG	41	-1250.6302	2741.5526	0.0002	1.0000
SYMG	41	-1253.5095	2747.3111	0.0000	1.0000
SYMI	41	-1254.8880	2750.0682	0.0000	1.0000
SYMIG	42	-1253.3149	2752.7828	0.0000	1.0000
GTRG	44	-1250.6425	2759.1596	0.0000	1.0000
K2P	36	-1274.3959	2759.7800	0.0000	1.0000
GTRI	44	-1252.2027	2762.2800	0.0000	1.0000
GTRIG	45	-1250.4911	2764.7177	0.0000	1.0000
HKY	39	-1270.9654	2770.5015	0.0000	1.0000
JC69G	36	-1283.7636	2778.5154	0.0000	1.0000
JC69I	36	-1283.9946	2778.9775	0.0000	1.0000
SYM	40	-1274.0990	2782.6295	0.0000	1.0000
JC69IG	37	-1283.6870	2784.2231	0.0000	1.0000
F81G	39	-1281.1068	2790.7842	0.0000	1.0000
F81I	39	-1281.3493	2791.2693	0.0000	1.0000
GTR	43	-1270.6416	2793.2971	0.0000	1.0000
F81IG	40	-1281.0453	2796.5220	0.0000	1.0000
JC69	35	-1302.2615	2809.6505	0.0000	1.0000
F81	38	-1299.3313	2821.3724	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/chr8_492.phylip = 1 - 351;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_492.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_492.phylip = 1 - 351;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_492.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;


[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/chr8_492.phylip = 1 - 351;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_492.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

