
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_4410.phylip" (19 taxa, 424 characters)

Minimum AIC  model: HKYG
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	-1127.4801	2343.5242	0.5380	0.5380
HKYIG	41	-1127.2000	2345.4156	0.2090	0.7470
HKYI	40	-1128.7095	2345.9830	0.1574	0.9043
GTRG	44	-1124.7809	2348.0104	0.0571	0.9614
GTRIG	45	-1124.5092	2349.9708	0.0214	0.9828
GTRI	44	-1126.0731	2350.5948	0.0157	0.9985
HKY	39	-1135.6258	2357.3766	0.0005	0.9991
K2PG	37	-1138.4074	2358.0997	0.0004	0.9994
F81G	39	-1136.8704	2359.8657	0.0002	0.9996
K2PIG	38	-1138.1797	2360.0581	0.0001	0.9997
K2PI	37	-1139.5104	2360.3058	0.0001	0.9998
F81IG	40	-1136.7014	2361.9667	0.0001	0.9999
F81I	39	-1138.0083	2362.1416	0.0000	0.9999
GTR	43	-1133.1685	2362.2950	0.0000	1.0000
SYMG	41	-1136.9986	2365.0129	0.0000	1.0000
SYMIG	42	-1136.7593	2366.9988	0.0000	1.0000
SYMI	41	-1138.1340	2367.2837	0.0000	1.0000
K2P	36	-1146.5536	2371.9909	0.0000	1.0000
JC69G	36	-1146.7818	2372.4473	0.0000	1.0000
F81	38	-1144.6410	2372.9807	0.0000	1.0000
JC69IG	37	-1146.5787	2374.4425	0.0000	1.0000
JC69I	36	-1147.8932	2374.6702	0.0000	1.0000
SYM	40	-1145.2737	2379.1113	0.0000	1.0000
JC69	35	-1154.6067	2385.7082	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1127.4801	2334.9603	0.4425	0.4425
HKYIG	41	-1127.2000	2336.3999	0.2154	0.6579
HKYI	40	-1128.7095	2337.4190	0.1294	0.7873
GTRG	44	-1124.7809	2337.5619	0.1205	0.9078
GTRIG	45	-1124.5092	2339.0184	0.0582	0.9660
GTRI	44	-1126.0731	2340.1463	0.0331	0.9991
HKY	39	-1135.6258	2349.2516	0.0003	0.9994
K2PG	37	-1138.4074	2350.8148	0.0002	0.9996
F81G	39	-1136.8704	2351.7407	0.0001	0.9997
GTR	43	-1133.1685	2352.3371	0.0001	0.9998
K2PIG	38	-1138.1797	2352.3594	0.0001	0.9998
K2PI	37	-1139.5104	2353.0209	0.0001	0.9999
F81IG	40	-1136.7014	2353.4027	0.0000	0.9999
F81I	39	-1138.0083	2354.0166	0.0000	1.0000
SYMG	41	-1136.9986	2355.9972	0.0000	1.0000
SYMIG	42	-1136.7593	2357.5185	0.0000	1.0000
SYMI	41	-1138.1340	2358.2680	0.0000	1.0000
K2P	36	-1146.5536	2365.1072	0.0000	1.0000
F81	38	-1144.6410	2365.2820	0.0000	1.0000
JC69G	36	-1146.7818	2365.5636	0.0000	1.0000
JC69IG	37	-1146.5787	2367.1575	0.0000	1.0000
JC69I	36	-1147.8932	2367.7864	0.0000	1.0000
SYM	40	-1145.2737	2370.5473	0.0000	1.0000
JC69	35	-1154.6067	2379.2134	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1127.4801	2496.9496	0.6307	0.6307
HKYI	40	-1128.7095	2499.4084	0.1845	0.8151
K2PG	37	-1138.4074	2500.6549	0.0989	0.9140
HKYIG	41	-1127.2000	2502.4390	0.0405	0.9546
K2PI	37	-1139.5104	2502.8610	0.0328	0.9874
K2PIG	38	-1138.1797	2506.2493	0.0060	0.9934
HKY	39	-1135.6258	2507.1912	0.0038	0.9972
F81G	39	-1136.8704	2509.6803	0.0011	0.9983
K2P	36	-1146.5536	2510.8976	0.0006	0.9989
JC69G	36	-1146.7818	2511.3540	0.0005	0.9993
F81I	39	-1138.0083	2511.9562	0.0003	0.9997
JC69I	36	-1147.8932	2513.5768	0.0002	0.9998
F81IG	40	-1136.7014	2515.3921	0.0001	0.9999
GTRG	44	-1124.7809	2515.7502	0.0001	0.9999
JC69IG	37	-1146.5787	2516.9976	0.0000	1.0000
GTRI	44	-1126.0731	2518.3346	0.0000	1.0000
F81	38	-1144.6410	2519.1719	0.0000	1.0000
JC69	35	-1154.6067	2520.9541	0.0000	1.0000
GTRIG	45	-1124.5092	2521.2564	0.0000	1.0000
SYMG	41	-1136.9986	2522.0363	0.0000	1.0000
SYMI	41	-1138.1340	2524.3071	0.0000	1.0000
GTR	43	-1133.1685	2526.4756	0.0000	1.0000
SYMIG	42	-1136.7593	2527.6073	0.0000	1.0000
SYM	40	-1145.2737	2532.5367	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_4410.phylip = 1 - 424;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4410.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4410.phylip = 1 - 424;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4410.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/chr8_4410.phylip = 1 - 424;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4410.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

