
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:12 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/chr11_1962.phylip" (19 taxa, 539 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
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
GTRI	44	-1503.1385	3102.2932	0.4117	0.4117
GTRG	44	-1503.2944	3102.6051	0.3522	0.7639
GTRIG	45	-1503.1369	3104.6713	0.1254	0.8892
HKYG	40	-1509.9925	3106.5713	0.0485	0.9377
HKYI	40	-1510.0361	3106.6586	0.0464	0.9841
HKYIG	41	-1509.9609	3108.8515	0.0155	0.9996
GTR	43	-1511.4603	3116.5650	0.0003	1.0000
HKY	39	-1518.4770	3121.2066	0.0000	1.0000
K2PG	37	-1532.2668	3144.1464	0.0000	1.0000
K2PIG	38	-1532.2024	3146.3329	0.0000	1.0000
SYMG	41	-1529.5425	3148.0146	0.0000	1.0000
K2PI	37	-1534.7385	3149.0897	0.0000	1.0000
SYMIG	42	-1531.0092	3153.3007	0.0000	1.0000
SYMI	41	-1533.1960	3155.3216	0.0000	1.0000
K2P	36	-1543.8187	3164.9442	0.0000	1.0000
SYM	40	-1540.5447	3167.6756	0.0000	1.0000
F81I	39	-1556.3191	3196.8907	0.0000	1.0000
F81G	39	-1556.3263	3196.9051	0.0000	1.0000
F81IG	40	-1556.2935	3199.1734	0.0000	1.0000
F81	38	-1563.9359	3209.7997	0.0000	1.0000
JC69G	36	-1572.4367	3222.1801	0.0000	1.0000
JC69IG	37	-1573.8946	3227.4020	0.0000	1.0000
JC69I	36	-1577.8046	3232.9160	0.0000	1.0000
JC69	35	-1584.4838	3243.9775	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1503.1385	3094.2770	0.4238	0.4238
GTRG	44	-1503.2944	3094.5889	0.3626	0.7865
GTRIG	45	-1503.1369	3096.2738	0.1562	0.9426
HKYG	40	-1509.9925	3099.9850	0.0244	0.9671
HKYI	40	-1510.0361	3100.0722	0.0234	0.9904
HKYIG	41	-1509.9609	3101.9219	0.0093	0.9997
GTR	43	-1511.4603	3108.9206	0.0003	1.0000
HKY	39	-1518.4770	3114.9541	0.0000	1.0000
K2PG	37	-1532.2668	3138.5336	0.0000	1.0000
K2PIG	38	-1532.2024	3140.4049	0.0000	1.0000
SYMG	41	-1529.5425	3141.0850	0.0000	1.0000
K2PI	37	-1534.7385	3143.4769	0.0000	1.0000
SYMIG	42	-1531.0092	3146.0184	0.0000	1.0000
SYMI	41	-1533.1960	3148.3920	0.0000	1.0000
K2P	36	-1543.8187	3159.6374	0.0000	1.0000
SYM	40	-1540.5447	3161.0893	0.0000	1.0000
F81I	39	-1556.3191	3190.6382	0.0000	1.0000
F81G	39	-1556.3263	3190.6526	0.0000	1.0000
F81IG	40	-1556.2935	3192.5871	0.0000	1.0000
F81	38	-1563.9359	3203.8717	0.0000	1.0000
JC69G	36	-1572.4367	3216.8734	0.0000	1.0000
JC69IG	37	-1573.8946	3221.7893	0.0000	1.0000
JC69I	36	-1577.8046	3227.6093	0.0000	1.0000
JC69	35	-1584.4838	3238.9675	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1509.9925	3271.5736	0.4968	0.4968
HKYI	40	-1510.0361	3271.6609	0.4756	0.9724
HKYIG	41	-1509.9609	3277.8002	0.0221	0.9945
HKY	39	-1518.4770	3282.2530	0.0024	0.9969
GTRI	44	-1503.1385	3283.0244	0.0016	0.9985
GTRG	44	-1503.2944	3283.3364	0.0014	0.9999
GTRIG	45	-1503.1369	3289.3110	0.0001	1.0000
GTR	43	-1511.4603	3293.3783	0.0000	1.0000
K2PG	37	-1532.2668	3297.2531	0.0000	1.0000
K2PI	37	-1534.7385	3302.1964	0.0000	1.0000
K2PIG	38	-1532.2024	3303.4141	0.0000	1.0000
K2P	36	-1543.8187	3314.0672	0.0000	1.0000
SYMG	41	-1529.5425	3316.9634	0.0000	1.0000
SYMI	41	-1533.1960	3324.2703	0.0000	1.0000
SYMIG	42	-1531.0092	3326.1865	0.0000	1.0000
SYM	40	-1540.5447	3332.6779	0.0000	1.0000
F81I	39	-1556.3191	3357.9371	0.0000	1.0000
F81G	39	-1556.3263	3357.9515	0.0000	1.0000
F81IG	40	-1556.2935	3364.1757	0.0000	1.0000
F81	38	-1563.9359	3366.8809	0.0000	1.0000
JC69G	36	-1572.4367	3371.3031	0.0000	1.0000
JC69IG	37	-1573.8946	3380.5087	0.0000	1.0000
JC69I	36	-1577.8046	3382.0390	0.0000	1.0000
JC69	35	-1584.4838	3389.1076	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1962.phylip = 1 - 539;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1962.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1962.phylip = 1 - 539;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1962.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr11_1962.phylip = 1 - 539;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_1962.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

