
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:38 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/chr24_938.phylip" (19 taxa, 328 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-1120.3998	2332.2282	0.4576	0.4576
GTRG	44	-1115.8104	2333.6137	0.2289	0.6865
HKYIG	41	-1119.9992	2334.0403	0.1849	0.8714
GTRIG	45	-1115.4192	2335.5193	0.0883	0.9597
HKYI	40	-1122.8726	2337.1738	0.0386	0.9983
GTRI	44	-1120.7656	2343.5241	0.0016	0.9999
K2PG	37	-1133.1961	2350.0888	0.0001	1.0000
K2PIG	38	-1132.7663	2351.7886	0.0000	1.0000
K2PI	37	-1135.5107	2354.7180	0.0000	1.0000
HKY	39	-1134.2105	2357.2544	0.0000	1.0000
SYMG	41	-1132.4273	2358.8966	0.0000	1.0000
SYMIG	42	-1131.9979	2360.6695	0.0000	1.0000
GTR	43	-1130.9591	2361.2422	0.0000	1.0000
SYMI	41	-1134.7904	2363.6227	0.0000	1.0000
F81G	39	-1145.4119	2379.6571	0.0000	1.0000
K2P	36	-1150.6567	2382.4680	0.0000	1.0000
F81IG	40	-1146.0945	2383.6175	0.0000	1.0000
F81I	39	-1147.4235	2383.6803	0.0000	1.0000
SYM	40	-1149.8099	2391.0484	0.0000	1.0000
JC69G	36	-1156.9010	2394.9567	0.0000	1.0000
JC69IG	37	-1156.5605	2396.8175	0.0000	1.0000
JC69I	36	-1159.1400	2399.4347	0.0000	1.0000
F81	38	-1160.5642	2407.3845	0.0000	1.0000
JC69	35	-1171.7341	2422.0984	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1115.8104	2319.6207	0.4070	0.4070
HKYG	40	-1120.3998	2320.7996	0.2257	0.6327
GTRIG	45	-1115.4192	2320.8385	0.2214	0.8541
HKYIG	41	-1119.9992	2321.9983	0.1240	0.9781
HKYI	40	-1122.8726	2325.7452	0.0190	0.9971
GTRI	44	-1120.7656	2329.5311	0.0029	1.0000
K2PG	37	-1133.1961	2340.3922	0.0000	1.0000
K2PIG	38	-1132.7663	2341.5326	0.0000	1.0000
K2PI	37	-1135.5107	2345.0214	0.0000	1.0000
HKY	39	-1134.2105	2346.4210	0.0000	1.0000
SYMG	41	-1132.4273	2346.8546	0.0000	1.0000
GTR	43	-1130.9591	2347.9183	0.0000	1.0000
SYMIG	42	-1131.9979	2347.9958	0.0000	1.0000
SYMI	41	-1134.7904	2351.5808	0.0000	1.0000
F81G	39	-1145.4119	2368.8237	0.0000	1.0000
F81IG	40	-1146.0945	2372.1889	0.0000	1.0000
F81I	39	-1147.4235	2372.8470	0.0000	1.0000
K2P	36	-1150.6567	2373.3134	0.0000	1.0000
SYM	40	-1149.8099	2379.6198	0.0000	1.0000
JC69G	36	-1156.9010	2385.8021	0.0000	1.0000
JC69IG	37	-1156.5605	2387.1210	0.0000	1.0000
JC69I	36	-1159.1400	2390.2801	0.0000	1.0000
F81	38	-1160.5642	2397.1284	0.0000	1.0000
JC69	35	-1171.7341	2413.4682	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1120.3998	2472.5201	0.8423	0.8423
HKYI	40	-1122.8726	2477.4657	0.0710	0.9133
HKYIG	41	-1119.9992	2477.5119	0.0694	0.9827
K2PG	37	-1133.1961	2480.7337	0.0139	0.9966
K2PI	37	-1135.5107	2485.3629	0.0014	0.9980
K2PIG	38	-1132.7663	2485.6671	0.0012	0.9991
GTRG	44	-1115.8104	2486.5133	0.0008	0.9999
GTRIG	45	-1115.4192	2491.5241	0.0001	1.0000
HKY	39	-1134.2105	2494.3486	0.0000	1.0000
GTRI	44	-1120.7656	2496.4237	0.0000	1.0000
SYMG	41	-1132.4273	2502.3682	0.0000	1.0000
SYMI	41	-1134.7904	2507.0943	0.0000	1.0000
SYMIG	42	-1131.9979	2507.3024	0.0000	1.0000
K2P	36	-1150.6567	2509.8618	0.0000	1.0000
GTR	43	-1130.9591	2511.0179	0.0000	1.0000
F81G	39	-1145.4119	2516.7513	0.0000	1.0000
F81I	39	-1147.4235	2520.7745	0.0000	1.0000
JC69G	36	-1156.9010	2522.3506	0.0000	1.0000
F81IG	40	-1146.0945	2523.9094	0.0000	1.0000
JC69I	36	-1159.1400	2526.8286	0.0000	1.0000
JC69IG	37	-1156.5605	2527.4625	0.0000	1.0000
SYM	40	-1149.8099	2531.3403	0.0000	1.0000
F81	38	-1160.5642	2541.2629	0.0000	1.0000
JC69	35	-1171.7341	2546.2237	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/chr24_938.phylip = 1 - 328;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_938.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_938.phylip = 1 - 328;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_938.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 BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_938.phylip = 1 - 328;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr24_938.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

