
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:01 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/chr1_25652.phylip" (19 taxa, 577 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	-1516.4631	3128.3697	0.5930	0.5930
GTRIG	45	-1516.1173	3130.0311	0.2584	0.8513
GTRI	44	-1517.9117	3131.2669	0.1393	0.9906
HKYG	40	-1525.8442	3137.8077	0.0053	0.9959
HKYIG	41	-1525.4780	3139.3933	0.0024	0.9983
HKYI	40	-1526.9880	3140.0955	0.0017	1.0000
GTR	43	-1529.1511	3151.4017	0.0000	1.0000
HKY	39	-1539.3172	3162.4444	0.0000	1.0000
SYMG	41	-1542.0874	3172.6122	0.0000	1.0000
K2PG	37	-1546.8557	3172.9284	0.0000	1.0000
SYMIG	42	-1541.6457	3174.0554	0.0000	1.0000
K2PIG	38	-1546.4206	3174.3504	0.0000	1.0000
SYMI	41	-1543.1335	3174.7043	0.0000	1.0000
K2PI	37	-1547.7570	3174.7310	0.0000	1.0000
F81G	39	-1550.9555	3185.7210	0.0000	1.0000
F81IG	40	-1550.5873	3187.2940	0.0000	1.0000
F81I	39	-1551.9926	3187.7953	0.0000	1.0000
SYM	40	-1556.2960	3198.7115	0.0000	1.0000
K2P	36	-1561.8028	3200.5389	0.0000	1.0000
F81	38	-1564.5351	3210.5795	0.0000	1.0000
JC69G	36	-1570.0357	3217.0047	0.0000	1.0000
JC69IG	37	-1569.6472	3218.5116	0.0000	1.0000
JC69I	36	-1570.9435	3218.8203	0.0000	1.0000
JC69	35	-1584.3146	3243.2873	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1516.4631	3120.9261	0.5671	0.5671
GTRIG	45	-1516.1173	3122.2345	0.2948	0.8620
GTRI	44	-1517.9117	3123.8233	0.1332	0.9952
HKYG	40	-1525.8442	3131.6883	0.0026	0.9978
HKYIG	41	-1525.4780	3132.9559	0.0014	0.9992
HKYI	40	-1526.9880	3133.9761	0.0008	1.0000
GTR	43	-1529.1511	3144.3022	0.0000	1.0000
HKY	39	-1539.3172	3156.6344	0.0000	1.0000
SYMG	41	-1542.0874	3166.1749	0.0000	1.0000
SYMIG	42	-1541.6457	3167.2914	0.0000	1.0000
K2PG	37	-1546.8557	3167.7113	0.0000	1.0000
SYMI	41	-1543.1335	3168.2669	0.0000	1.0000
K2PIG	38	-1546.4206	3168.8411	0.0000	1.0000
K2PI	37	-1547.7570	3169.5139	0.0000	1.0000
F81G	39	-1550.9555	3179.9109	0.0000	1.0000
F81IG	40	-1550.5873	3181.1746	0.0000	1.0000
F81I	39	-1551.9926	3181.9852	0.0000	1.0000
SYM	40	-1556.2960	3192.5921	0.0000	1.0000
K2P	36	-1561.8028	3195.6056	0.0000	1.0000
F81	38	-1564.5351	3205.0702	0.0000	1.0000
JC69G	36	-1570.0357	3212.0713	0.0000	1.0000
JC69IG	37	-1569.6472	3213.2945	0.0000	1.0000
JC69I	36	-1570.9435	3213.8870	0.0000	1.0000
JC69	35	-1584.3146	3238.6292	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1525.8442	3306.0020	0.7019	0.7019
HKYI	40	-1526.9880	3308.2898	0.2236	0.9255
HKYIG	41	-1525.4780	3311.6275	0.0421	0.9676
GTRG	44	-1516.4631	3312.6712	0.0250	0.9926
GTRI	44	-1517.9117	3315.5684	0.0059	0.9985
GTRIG	45	-1516.1173	3318.3374	0.0015	1.0000
HKY	39	-1539.3172	3326.5902	0.0000	1.0000
K2PG	37	-1546.8557	3328.9515	0.0000	1.0000
K2PI	37	-1547.7570	3330.7541	0.0000	1.0000
GTR	43	-1529.1511	3331.6894	0.0000	1.0000
K2PIG	38	-1546.4206	3334.4391	0.0000	1.0000
SYMG	41	-1542.0874	3344.8464	0.0000	1.0000
SYMI	41	-1543.1335	3346.9385	0.0000	1.0000
F81G	39	-1550.9555	3349.8668	0.0000	1.0000
SYMIG	42	-1541.6457	3350.3208	0.0000	1.0000
F81I	39	-1551.9926	3351.9411	0.0000	1.0000
K2P	36	-1561.8028	3352.4879	0.0000	1.0000
F81IG	40	-1550.5873	3355.4883	0.0000	1.0000
SYM	40	-1556.2960	3366.9058	0.0000	1.0000
JC69G	36	-1570.0357	3368.9537	0.0000	1.0000
F81	38	-1564.5351	3370.6682	0.0000	1.0000
JC69I	36	-1570.9435	3370.7693	0.0000	1.0000
JC69IG	37	-1569.6472	3374.5347	0.0000	1.0000
JC69	35	-1584.3146	3391.1537	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/chr1_25652.phylip = 1 - 577;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25652.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/chr1_25652.phylip = 1 - 577;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25652.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/chr1_25652.phylip = 1 - 577;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_25652.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

