
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:07 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/chr7_4698.phylip" (19 taxa, 960 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-2474.9928	5044.5151	0.5572	0.5572
GTRG	44	-2476.8957	5046.1193	0.2498	0.8070
GTRI	44	-2477.2658	5046.8594	0.1726	0.9795
HKYIG	41	-2483.2110	5052.1736	0.0121	0.9916
HKYG	40	-2485.1646	5053.8982	0.0051	0.9967
HKYI	40	-2485.6171	5054.8032	0.0033	1.0000
SYMIG	42	-2492.4095	5072.7580	0.0000	1.0000
K2PG	37	-2498.1481	5073.3460	0.0000	1.0000
K2PIG	38	-2497.1016	5073.4215	0.0000	1.0000
SYMG	41	-2494.1786	5074.1088	0.0000	1.0000
SYMI	41	-2494.5942	5074.9400	0.0000	1.0000
K2PI	37	-2499.3800	5075.8099	0.0000	1.0000
F81IG	40	-2517.5580	5118.6852	0.0000	1.0000
F81G	39	-2519.1717	5119.7348	0.0000	1.0000
F81I	39	-2519.6335	5120.6584	0.0000	1.0000
GTR	43	-2521.9072	5133.9454	0.0000	1.0000
JC69G	36	-2530.1304	5135.1470	0.0000	1.0000
JC69IG	37	-2529.2275	5135.5049	0.0000	1.0000
JC69I	36	-2531.2717	5137.4297	0.0000	1.0000
HKY	39	-2528.3201	5138.0316	0.0000	1.0000
K2P	36	-2540.5263	5155.9389	0.0000	1.0000
SYM	40	-2536.8680	5157.3051	0.0000	1.0000
F81	38	-2561.1280	5201.4743	0.0000	1.0000
JC69	35	-2571.7286	5216.1845	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-2474.9928	5039.9855	0.5850	0.5850
GTRG	44	-2476.8957	5041.7914	0.2371	0.8222
GTRI	44	-2477.2658	5042.5315	0.1638	0.9860
HKYIG	41	-2483.2110	5048.4219	0.0086	0.9946
HKYG	40	-2485.1646	5050.3291	0.0033	0.9979
HKYI	40	-2485.6171	5051.2341	0.0021	1.0000
SYMIG	42	-2492.4095	5068.8190	0.0000	1.0000
K2PIG	38	-2497.1016	5070.2033	0.0000	1.0000
K2PG	37	-2498.1481	5070.2961	0.0000	1.0000
SYMG	41	-2494.1786	5070.3572	0.0000	1.0000
SYMI	41	-2494.5942	5071.1883	0.0000	1.0000
K2PI	37	-2499.3800	5072.7600	0.0000	1.0000
F81IG	40	-2517.5580	5115.1161	0.0000	1.0000
F81G	39	-2519.1717	5116.3435	0.0000	1.0000
F81I	39	-2519.6335	5117.2671	0.0000	1.0000
GTR	43	-2521.9072	5129.8144	0.0000	1.0000
JC69G	36	-2530.1304	5132.2608	0.0000	1.0000
JC69IG	37	-2529.2275	5132.4550	0.0000	1.0000
JC69I	36	-2531.2717	5134.5435	0.0000	1.0000
HKY	39	-2528.3201	5134.6403	0.0000	1.0000
K2P	36	-2540.5263	5153.0526	0.0000	1.0000
SYM	40	-2536.8680	5153.7360	0.0000	1.0000
F81	38	-2561.1280	5198.2560	0.0000	1.0000
JC69	35	-2571.7286	5213.4572	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2485.1646	5245.0065	0.5086	0.5086
HKYI	40	-2485.6171	5245.9115	0.3235	0.8320
HKYIG	41	-2483.2110	5247.9662	0.1158	0.9478
K2PG	37	-2498.1481	5250.3727	0.0348	0.9826
K2PI	37	-2499.3800	5252.8365	0.0101	0.9927
K2PIG	38	-2497.1016	5255.1467	0.0032	0.9959
GTRG	44	-2476.8957	5255.9365	0.0022	0.9980
GTRI	44	-2477.2658	5256.6766	0.0015	0.9995
GTRIG	45	-2474.9928	5258.9975	0.0005	1.0000
SYMG	41	-2494.1786	5269.9015	0.0000	1.0000
SYMI	41	-2494.5942	5270.7326	0.0000	1.0000
SYMIG	42	-2492.4095	5273.2302	0.0000	1.0000
F81G	39	-2519.1717	5306.1539	0.0000	1.0000
F81I	39	-2519.6335	5307.0775	0.0000	1.0000
JC69G	36	-2530.1304	5307.4704	0.0000	1.0000
JC69I	36	-2531.2717	5309.7531	0.0000	1.0000
F81IG	40	-2517.5580	5309.7934	0.0000	1.0000
JC69IG	37	-2529.2275	5312.5315	0.0000	1.0000
HKY	39	-2528.3201	5324.4507	0.0000	1.0000
K2P	36	-2540.5263	5328.2622	0.0000	1.0000
GTR	43	-2521.9072	5339.0925	0.0000	1.0000
SYM	40	-2536.8680	5348.4133	0.0000	1.0000
F81	38	-2561.1280	5383.1995	0.0000	1.0000
JC69	35	-2571.7286	5383.7999	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4698.phylip = 1 - 960;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4698.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4698.phylip = 1 - 960;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4698.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) 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/chr7_4698.phylip = 1 - 960;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4698.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

