
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:22 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_3186.phylip" (19 taxa, 1068 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	-3965.2873	8022.4456	0.7468	0.7468
GTRIG	45	-3965.5955	8025.2419	0.1845	0.9313
HKYG	40	-3972.5960	8028.3857	0.0383	0.9696
HKYIG	41	-3971.7474	8028.8515	0.0304	1.0000
GTRI	44	-3984.0064	8059.8838	0.0000	1.0000
HKYI	40	-3988.5245	8060.2428	0.0000	1.0000
K2PG	37	-4029.6200	8135.9701	0.0000	1.0000
K2PIG	38	-4029.2006	8137.2816	0.0000	1.0000
SYMG	41	-4028.5454	8142.4475	0.0000	1.0000
SYMIG	42	-4027.8791	8143.2820	0.0000	1.0000
K2PI	37	-4044.3523	8165.4348	0.0000	1.0000
SYMI	41	-4042.9920	8171.3408	0.0000	1.0000
F81G	39	-4063.8507	8208.7365	0.0000	1.0000
F81IG	40	-4063.1577	8209.5091	0.0000	1.0000
F81I	39	-4078.1457	8237.3265	0.0000	1.0000
HKY	39	-4083.5914	8248.2179	0.0000	1.0000
GTR	43	-4081.1196	8251.9346	0.0000	1.0000
JC69G	36	-4104.4451	8283.4741	0.0000	1.0000
JC69IG	37	-4103.8384	8284.4070	0.0000	1.0000
JC69I	36	-4118.3256	8311.2351	0.0000	1.0000
K2P	36	-4135.2429	8345.0698	0.0000	1.0000
SYM	40	-4134.1137	8351.4212	0.0000	1.0000
F81	38	-4167.7673	8414.4151	0.0000	1.0000
JC69	35	-4206.2336	8484.9090	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3965.2873	8018.5746	0.7472	0.7472
GTRIG	45	-3965.5955	8021.1910	0.2020	0.9492
HKYG	40	-3972.5960	8025.1919	0.0273	0.9765
HKYIG	41	-3971.7474	8025.4948	0.0235	1.0000
GTRI	44	-3984.0064	8056.0129	0.0000	1.0000
HKYI	40	-3988.5245	8057.0491	0.0000	1.0000
K2PG	37	-4029.6200	8133.2400	0.0000	1.0000
K2PIG	38	-4029.2006	8134.4011	0.0000	1.0000
SYMG	41	-4028.5454	8139.0908	0.0000	1.0000
SYMIG	42	-4027.8791	8139.7581	0.0000	1.0000
K2PI	37	-4044.3523	8162.7047	0.0000	1.0000
SYMI	41	-4042.9920	8167.9841	0.0000	1.0000
F81G	39	-4063.8507	8205.7014	0.0000	1.0000
F81IG	40	-4063.1577	8206.3154	0.0000	1.0000
F81I	39	-4078.1457	8234.2914	0.0000	1.0000
HKY	39	-4083.5914	8245.1829	0.0000	1.0000
GTR	43	-4081.1196	8248.2393	0.0000	1.0000
JC69G	36	-4104.4451	8280.8902	0.0000	1.0000
JC69IG	37	-4103.8384	8281.6769	0.0000	1.0000
JC69I	36	-4118.3256	8308.6512	0.0000	1.0000
K2P	36	-4135.2429	8342.4859	0.0000	1.0000
SYM	40	-4134.1137	8348.2274	0.0000	1.0000
F81	38	-4167.7673	8411.5347	0.0000	1.0000
JC69	35	-4206.2336	8482.4671	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3972.5960	8224.1337	0.9321	0.9321
HKYIG	41	-3971.7474	8229.4101	0.0666	0.9988
GTRG	44	-3965.2873	8237.4105	0.0012	1.0000
GTRIG	45	-3965.5955	8245.0004	0.0000	1.0000
HKYI	40	-3988.5245	8255.9908	0.0000	1.0000
GTRI	44	-3984.0064	8274.8488	0.0000	1.0000
K2PG	37	-4029.6200	8317.2611	0.0000	1.0000
K2PIG	38	-4029.2006	8323.3957	0.0000	1.0000
SYMG	41	-4028.5454	8343.0060	0.0000	1.0000
K2PI	37	-4044.3523	8346.7258	0.0000	1.0000
SYMIG	42	-4027.8791	8348.6469	0.0000	1.0000
SYMI	41	-4042.9920	8371.8993	0.0000	1.0000
F81G	39	-4063.8507	8399.6696	0.0000	1.0000
F81IG	40	-4063.1577	8405.2571	0.0000	1.0000
F81I	39	-4078.1457	8428.2596	0.0000	1.0000
HKY	39	-4083.5914	8439.1511	0.0000	1.0000
JC69G	36	-4104.4451	8459.9378	0.0000	1.0000
GTR	43	-4081.1196	8462.1016	0.0000	1.0000
JC69IG	37	-4103.8384	8465.6980	0.0000	1.0000
JC69I	36	-4118.3256	8487.6987	0.0000	1.0000
K2P	36	-4135.2429	8521.5334	0.0000	1.0000
SYM	40	-4134.1137	8547.1691	0.0000	1.0000
F81	38	-4167.7673	8600.5293	0.0000	1.0000
JC69	35	-4206.2336	8656.5411	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_3186.phylip = 1 - 1068;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3186.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_3186.phylip = 1 - 1068;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3186.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_3186.phylip = 1 - 1068;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3186.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

