
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:31 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/chr4_6778.phylip" (19 taxa, 382 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	-1010.8380	2111.2948	0.2862	0.2862
GTRG	44	-1005.8995	2111.5498	0.2519	0.5381
HKYI	40	-1011.4324	2112.4835	0.1579	0.6960
GTRI	44	-1006.4648	2112.6804	0.1431	0.8391
HKYIG	41	-1010.7820	2113.6933	0.0863	0.9254
GTRIG	45	-1005.8356	2113.9926	0.0743	0.9996
HKY	39	-1019.3731	2125.8690	0.0002	0.9998
GTR	43	-1014.6948	2126.5849	0.0001	1.0000
K2PG	37	-1025.2006	2132.5756	0.0000	1.0000
SYMG	41	-1020.4779	2133.0852	0.0000	1.0000
K2PI	37	-1025.8322	2133.8389	0.0000	1.0000
SYMI	41	-1021.1903	2134.5100	0.0000	1.0000
K2PIG	38	-1025.1384	2134.9183	0.0000	1.0000
SYMIG	42	-1020.3949	2135.4447	0.0000	1.0000
F81G	39	-1026.4844	2140.0915	0.0000	1.0000
F81I	39	-1026.9945	2141.1119	0.0000	1.0000
F81IG	40	-1026.4567	2142.5322	0.0000	1.0000
K2P	36	-1033.3151	2146.3520	0.0000	1.0000
SYM	40	-1028.8638	2147.3464	0.0000	1.0000
F81	38	-1033.8797	2152.4008	0.0000	1.0000
JC69G	36	-1039.5536	2158.8289	0.0000	1.0000
JC69I	36	-1040.0936	2159.9089	0.0000	1.0000
JC69IG	37	-1039.5220	2161.2184	0.0000	1.0000
JC69	35	-1046.9836	2171.2505	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1005.8995	2099.7990	0.3676	0.3676
GTRI	44	-1006.4648	2100.9297	0.2089	0.5765
GTRIG	45	-1005.8356	2101.6712	0.1442	0.7206
HKYG	40	-1010.8380	2101.6760	0.1438	0.8644
HKYI	40	-1011.4324	2102.8647	0.0794	0.9438
HKYIG	41	-1010.7820	2103.5639	0.0560	0.9998
GTR	43	-1014.6948	2115.3896	0.0002	0.9999
HKY	39	-1019.3731	2116.7462	0.0001	1.0000
SYMG	41	-1020.4779	2122.9558	0.0000	1.0000
SYMI	41	-1021.1903	2124.3806	0.0000	1.0000
K2PG	37	-1025.2006	2124.4012	0.0000	1.0000
SYMIG	42	-1020.3949	2124.7898	0.0000	1.0000
K2PI	37	-1025.8322	2125.6645	0.0000	1.0000
K2PIG	38	-1025.1384	2126.2769	0.0000	1.0000
F81G	39	-1026.4844	2130.9687	0.0000	1.0000
F81I	39	-1026.9945	2131.9891	0.0000	1.0000
F81IG	40	-1026.4567	2132.9135	0.0000	1.0000
SYM	40	-1028.8638	2137.7277	0.0000	1.0000
K2P	36	-1033.3151	2138.6303	0.0000	1.0000
F81	38	-1033.8797	2143.7594	0.0000	1.0000
JC69G	36	-1039.5536	2151.1071	0.0000	1.0000
JC69I	36	-1040.0936	2152.1871	0.0000	1.0000
JC69IG	37	-1039.5220	2153.0439	0.0000	1.0000
JC69	35	-1046.9836	2163.9673	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1010.8380	2259.4928	0.6179	0.6179
HKYI	40	-1011.4324	2260.6815	0.3410	0.9590
HKYIG	41	-1010.7820	2265.3262	0.0334	0.9924
K2PG	37	-1025.2006	2270.3817	0.0027	0.9951
HKY	39	-1019.3731	2270.6176	0.0024	0.9975
K2PI	37	-1025.8322	2271.6450	0.0014	0.9989
GTRG	44	-1005.8995	2273.3975	0.0006	0.9995
GTRI	44	-1006.4648	2274.5282	0.0003	0.9998
K2PIG	38	-1025.1384	2276.2029	0.0001	0.9999
GTRIG	45	-1005.8356	2279.2151	0.0000	1.0000
K2P	36	-1033.3151	2280.6654	0.0000	1.0000
SYMG	41	-1020.4779	2284.7180	0.0000	1.0000
F81G	39	-1026.4844	2284.8401	0.0000	1.0000
GTR	43	-1014.6948	2285.0427	0.0000	1.0000
F81I	39	-1026.9945	2285.8605	0.0000	1.0000
SYMI	41	-1021.1903	2286.1428	0.0000	1.0000
SYMIG	42	-1020.3949	2290.4975	0.0000	1.0000
F81IG	40	-1026.4567	2290.7303	0.0000	1.0000
JC69G	36	-1039.5536	2293.1423	0.0000	1.0000
F81	38	-1033.8797	2293.6854	0.0000	1.0000
JC69I	36	-1040.0936	2294.2223	0.0000	1.0000
SYM	40	-1028.8638	2295.5445	0.0000	1.0000
JC69IG	37	-1039.5220	2299.0245	0.0000	1.0000
JC69	35	-1046.9836	2302.0570	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/chr4_6778.phylip = 1 - 382;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_6778.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/chr4_6778.phylip = 1 - 382;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_6778.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/chr4_6778.phylip = 1 - 382;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_6778.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

