
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:29 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/chr5_1800.phylip" (19 taxa, 635 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	-2064.2147	4223.1413	0.8922	0.8922
GTRIG	45	-2065.6744	4228.3777	0.0651	0.9573
GTRI	44	-2067.2737	4229.2592	0.0419	0.9991
HKYG	40	-2076.0136	4237.5490	0.0007	0.9998
HKYI	40	-2077.7883	4241.0985	0.0001	0.9999
HKYIG	41	-2076.8677	4241.5431	0.0001	1.0000
SYMG	41	-2088.5781	4264.9640	0.0000	1.0000
SYMIG	42	-2088.6511	4267.4036	0.0000	1.0000
SYMI	41	-2090.3172	4268.4421	0.0000	1.0000
K2PG	37	-2097.7027	4274.1156	0.0000	1.0000
K2PIG	38	-2097.4960	4275.9652	0.0000	1.0000
K2PI	37	-2099.5530	4277.8163	0.0000	1.0000
GTR	43	-2098.7748	4289.9524	0.0000	1.0000
HKY	39	-2110.1918	4303.6272	0.0000	1.0000
SYM	40	-2124.3333	4334.1886	0.0000	1.0000
F81G	39	-2127.1129	4337.4695	0.0000	1.0000
F81I	39	-2127.8931	4339.0298	0.0000	1.0000
F81IG	40	-2126.9078	4339.3375	0.0000	1.0000
K2P	36	-2132.4783	4341.4115	0.0000	1.0000
JC69G	36	-2144.9990	4366.4529	0.0000	1.0000
JC69IG	37	-2144.8362	4368.3826	0.0000	1.0000
JC69I	36	-2146.5486	4369.5521	0.0000	1.0000
F81	38	-2159.7278	4400.4287	0.0000	1.0000
JC69	35	-2178.4753	4431.1576	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2064.2147	4216.4295	0.8827	0.8827
GTRIG	45	-2065.6744	4221.3488	0.0754	0.9581
GTRI	44	-2067.2737	4222.5473	0.0414	0.9995
HKYG	40	-2076.0136	4232.0271	0.0004	0.9999
HKYI	40	-2077.7883	4235.5767	0.0001	0.9999
HKYIG	41	-2076.8677	4235.7354	0.0001	1.0000
SYMG	41	-2088.5781	4259.1563	0.0000	1.0000
SYMIG	42	-2088.6511	4261.3022	0.0000	1.0000
SYMI	41	-2090.3172	4262.6344	0.0000	1.0000
K2PG	37	-2097.7027	4269.4053	0.0000	1.0000
K2PIG	38	-2097.4960	4270.9920	0.0000	1.0000
K2PI	37	-2099.5530	4273.1061	0.0000	1.0000
GTR	43	-2098.7748	4283.5497	0.0000	1.0000
HKY	39	-2110.1918	4298.3835	0.0000	1.0000
SYM	40	-2124.3333	4328.6667	0.0000	1.0000
F81G	39	-2127.1129	4332.2258	0.0000	1.0000
F81I	39	-2127.8931	4333.7861	0.0000	1.0000
F81IG	40	-2126.9078	4333.8156	0.0000	1.0000
K2P	36	-2132.4783	4336.9566	0.0000	1.0000
JC69G	36	-2144.9990	4361.9981	0.0000	1.0000
JC69IG	37	-2144.8362	4363.6724	0.0000	1.0000
JC69I	36	-2146.5486	4365.0972	0.0000	1.0000
F81	38	-2159.7278	4395.4555	0.0000	1.0000
JC69	35	-2178.4753	4426.9506	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2076.0136	4410.1721	0.6514	0.6514
GTRG	44	-2064.2147	4412.3890	0.2150	0.8665
HKYI	40	-2077.7883	4413.7217	0.1104	0.9769
HKYIG	41	-2076.8677	4418.3340	0.0110	0.9879
GTRI	44	-2067.2737	4418.5068	0.0101	0.9980
GTRIG	45	-2065.6744	4421.7619	0.0020	1.0000
K2PG	37	-2097.7027	4434.1895	0.0000	1.0000
K2PI	37	-2099.5530	4437.8902	0.0000	1.0000
K2PIG	38	-2097.4960	4440.2298	0.0000	1.0000
SYMG	41	-2088.5781	4441.7549	0.0000	1.0000
SYMI	41	-2090.3172	4445.2330	0.0000	1.0000
SYMIG	42	-2088.6511	4448.3544	0.0000	1.0000
HKY	39	-2110.1918	4472.0749	0.0000	1.0000
GTR	43	-2098.7748	4475.0556	0.0000	1.0000
K2P	36	-2132.4783	4497.2871	0.0000	1.0000
F81G	39	-2127.1129	4505.9172	0.0000	1.0000
SYM	40	-2124.3333	4506.8117	0.0000	1.0000
F81I	39	-2127.8931	4507.4775	0.0000	1.0000
F81IG	40	-2126.9078	4511.9606	0.0000	1.0000
JC69G	36	-2144.9990	4522.3286	0.0000	1.0000
JC69I	36	-2146.5486	4525.4277	0.0000	1.0000
JC69IG	37	-2144.8362	4528.4565	0.0000	1.0000
F81	38	-2159.7278	4564.6933	0.0000	1.0000
JC69	35	-2178.4753	4582.8275	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/chr5_1800.phylip = 1 - 635;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1800.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/chr5_1800.phylip = 1 - 635;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1800.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/chr5_1800.phylip = 1 - 635;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_1800.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

