
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/chr11_3414.phylip" (19 taxa, 428 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	-1054.4655	2207.2704	0.5779	0.5779
GTRI	44	-1055.4615	2209.2623	0.2135	0.7914
GTRIG	45	-1054.2665	2209.3707	0.2022	0.9936
HKYG	40	-1064.7491	2217.9736	0.0027	0.9963
HKYI	40	-1065.4087	2219.2929	0.0014	0.9977
GTR	43	-1061.7883	2219.4307	0.0013	0.9990
HKYIG	41	-1064.5691	2220.0605	0.0010	1.0000
HKY	39	-1072.4830	2231.0073	0.0000	1.0000
F81G	39	-1082.5590	2251.1593	0.0000	1.0000
F81I	39	-1083.1986	2252.4385	0.0000	1.0000
F81IG	40	-1082.3151	2253.1057	0.0000	1.0000
SYMG	41	-1083.0828	2257.0880	0.0000	1.0000
K2PG	37	-1088.0782	2257.3667	0.0000	1.0000
K2PI	37	-1088.6174	2258.4450	0.0000	1.0000
SYMI	41	-1083.7666	2258.4554	0.0000	1.0000
SYMIG	42	-1082.8418	2259.0654	0.0000	1.0000
K2PIG	38	-1087.8448	2259.3092	0.0000	1.0000
F81	38	-1090.5595	2264.7386	0.0000	1.0000
SYM	40	-1090.9340	2270.3434	0.0000	1.0000
K2P	36	-1096.8670	2272.5473	0.0000	1.0000
JC69G	36	-1103.0277	2284.8687	0.0000	1.0000
JC69I	36	-1103.6146	2286.0426	0.0000	1.0000
JC69IG	37	-1102.7502	2286.7107	0.0000	1.0000
JC69	35	-1111.5862	2299.6010	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1054.4655	2196.9309	0.5483	0.5483
GTRIG	45	-1054.2665	2198.5330	0.2461	0.7945
GTRI	44	-1055.4615	2198.9229	0.2025	0.9970
HKYG	40	-1064.7491	2209.4981	0.0010	0.9980
GTR	43	-1061.7883	2209.5765	0.0010	0.9990
HKYI	40	-1065.4087	2210.8175	0.0005	0.9995
HKYIG	41	-1064.5691	2211.1382	0.0005	1.0000
HKY	39	-1072.4830	2222.9661	0.0000	1.0000
F81G	39	-1082.5590	2243.1180	0.0000	1.0000
F81I	39	-1083.1986	2244.3972	0.0000	1.0000
F81IG	40	-1082.3151	2244.6302	0.0000	1.0000
SYMG	41	-1083.0828	2248.1657	0.0000	1.0000
SYMI	41	-1083.7666	2249.5331	0.0000	1.0000
SYMIG	42	-1082.8418	2249.6836	0.0000	1.0000
K2PG	37	-1088.0782	2250.1564	0.0000	1.0000
K2PI	37	-1088.6174	2251.2347	0.0000	1.0000
K2PIG	38	-1087.8448	2251.6897	0.0000	1.0000
F81	38	-1090.5595	2257.1190	0.0000	1.0000
SYM	40	-1090.9340	2261.8680	0.0000	1.0000
K2P	36	-1096.8670	2265.7340	0.0000	1.0000
JC69G	36	-1103.0277	2278.0554	0.0000	1.0000
JC69I	36	-1103.6146	2279.2293	0.0000	1.0000
JC69IG	37	-1102.7502	2279.5004	0.0000	1.0000
JC69	35	-1111.5862	2293.1724	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1064.7491	2371.8630	0.5512	0.5512
HKYI	40	-1065.4087	2373.1824	0.2850	0.8362
GTRG	44	-1054.4655	2375.5324	0.0880	0.9242
GTRI	44	-1055.4615	2377.5243	0.0325	0.9567
HKYIG	41	-1064.5691	2377.5623	0.0319	0.9886
GTRIG	45	-1054.2665	2381.1935	0.0052	0.9938
HKY	39	-1072.4830	2381.2719	0.0050	0.9988
GTR	43	-1061.7883	2384.1188	0.0012	1.0000
K2PG	37	-1088.0782	2400.3440	0.0000	1.0000
K2PI	37	-1088.6174	2401.4223	0.0000	1.0000
F81G	39	-1082.5590	2401.4238	0.0000	1.0000
F81I	39	-1083.1986	2402.7030	0.0000	1.0000
K2PIG	38	-1087.8448	2405.9364	0.0000	1.0000
F81IG	40	-1082.3151	2406.9952	0.0000	1.0000
F81	38	-1090.5595	2411.3657	0.0000	1.0000
K2P	36	-1096.8670	2411.8624	0.0000	1.0000
SYMG	41	-1083.0828	2414.5897	0.0000	1.0000
SYMI	41	-1083.7666	2415.9572	0.0000	1.0000
SYMIG	42	-1082.8418	2420.1668	0.0000	1.0000
JC69G	36	-1103.0277	2424.1838	0.0000	1.0000
SYM	40	-1090.9340	2424.2329	0.0000	1.0000
JC69I	36	-1103.6146	2425.3577	0.0000	1.0000
JC69IG	37	-1102.7502	2429.6880	0.0000	1.0000
JC69	35	-1111.5862	2435.2418	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/chr11_3414.phylip = 1 - 428;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3414.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/chr11_3414.phylip = 1 - 428;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3414.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/chr11_3414.phylip = 1 - 428;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3414.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

