
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:18 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_13362.phylip" (19 taxa, 694 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
Minimum BIC  model: HKYI


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
GTRIG	45	-1541.7556	3179.9000	0.7013	0.7013
HKYI	40	-1548.6316	3182.2862	0.2127	0.9141
GTRI	44	-1545.1974	3184.4966	0.0704	0.9845
HKYG	40	-1551.8853	3188.7935	0.0082	0.9927
GTRG	44	-1548.0492	3190.2001	0.0041	0.9968
HKYIG	41	-1551.6912	3190.6646	0.0032	1.0000
K2PI	37	-1565.4190	3209.1247	0.0000	1.0000
SYMIG	42	-1561.6925	3212.9334	0.0000	1.0000
SYMI	41	-1564.2127	3215.7076	0.0000	1.0000
K2PG	37	-1570.3000	3218.8866	0.0000	1.0000
K2PIG	38	-1569.8457	3220.2165	0.0000	1.0000
SYMG	41	-1568.6238	3224.5298	0.0000	1.0000
F81IG	40	-1574.5562	3234.1353	0.0000	1.0000
F81I	39	-1576.9794	3236.7293	0.0000	1.0000
F81G	39	-1581.0089	3244.7885	0.0000	1.0000
JC69IG	37	-1591.1133	3260.5131	0.0000	1.0000
GTR	43	-1584.5107	3260.8430	0.0000	1.0000
HKY	39	-1589.0834	3260.9374	0.0000	1.0000
JC69I	36	-1593.4798	3263.0144	0.0000	1.0000
JC69G	36	-1598.0933	3272.2414	0.0000	1.0000
K2P	36	-1609.1246	3294.3039	0.0000	1.0000
SYM	40	-1606.6761	3298.3751	0.0000	1.0000
F81	38	-1618.5971	3317.7194	0.0000	1.0000
JC69	35	-1636.5184	3346.8666	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1541.7556	3173.5111	0.7976	0.7976
HKYI	40	-1548.6316	3177.2633	0.1222	0.9198
GTRI	44	-1545.1974	3178.3949	0.0694	0.9892
HKYG	40	-1551.8853	3183.7705	0.0047	0.9939
GTRG	44	-1548.0492	3184.0984	0.0040	0.9979
HKYIG	41	-1551.6912	3185.3824	0.0021	1.0000
K2PI	37	-1565.4190	3204.8381	0.0000	1.0000
SYMIG	42	-1561.6925	3207.3850	0.0000	1.0000
SYMI	41	-1564.2127	3210.4254	0.0000	1.0000
K2PG	37	-1570.3000	3214.6000	0.0000	1.0000
K2PIG	38	-1569.8457	3215.6913	0.0000	1.0000
SYMG	41	-1568.6238	3219.2476	0.0000	1.0000
F81IG	40	-1574.5562	3229.1123	0.0000	1.0000
F81I	39	-1576.9794	3231.9587	0.0000	1.0000
F81G	39	-1581.0089	3240.0179	0.0000	1.0000
GTR	43	-1584.5107	3255.0214	0.0000	1.0000
HKY	39	-1589.0834	3256.1667	0.0000	1.0000
JC69IG	37	-1591.1133	3256.2266	0.0000	1.0000
JC69I	36	-1593.4798	3258.9596	0.0000	1.0000
JC69G	36	-1598.0933	3268.1866	0.0000	1.0000
K2P	36	-1609.1246	3290.2491	0.0000	1.0000
SYM	40	-1606.6761	3293.3521	0.0000	1.0000
F81	38	-1618.5971	3313.1942	0.0000	1.0000
JC69	35	-1636.5184	3343.0368	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1548.6316	3358.9621	0.9602	0.9602
HKYG	40	-1551.8853	3365.4694	0.0371	0.9972
HKYIG	41	-1551.6912	3371.6238	0.0017	0.9990
K2PI	37	-1565.4190	3372.9096	0.0009	0.9999
GTRIG	45	-1541.7556	3377.9224	0.0001	0.9999
GTRI	44	-1545.1974	3378.2636	0.0001	1.0000
K2PG	37	-1570.3000	3382.6715	0.0000	1.0000
GTRG	44	-1548.0492	3383.9672	0.0000	1.0000
K2PIG	38	-1569.8457	3388.3053	0.0000	1.0000
SYMI	41	-1564.2127	3396.6667	0.0000	1.0000
SYMIG	42	-1561.6925	3398.1688	0.0000	1.0000
SYMG	41	-1568.6238	3405.4890	0.0000	1.0000
F81I	39	-1576.9794	3409.1151	0.0000	1.0000
F81IG	40	-1574.5562	3410.8112	0.0000	1.0000
F81G	39	-1581.0089	3417.1743	0.0000	1.0000
JC69I	36	-1593.4798	3422.4886	0.0000	1.0000
JC69IG	37	-1591.1133	3424.2980	0.0000	1.0000
JC69G	36	-1598.0933	3431.7156	0.0000	1.0000
HKY	39	-1589.0834	3433.3231	0.0000	1.0000
GTR	43	-1584.5107	3450.3477	0.0000	1.0000
K2P	36	-1609.1246	3453.7781	0.0000	1.0000
SYM	40	-1606.6761	3475.0510	0.0000	1.0000
F81	38	-1618.5971	3485.8081	0.0000	1.0000
JC69	35	-1636.5184	3502.0234	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13362.phylip = 1 - 694;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13362.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13362.phylip = 1 - 694;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13362.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13362.phylip = 1 - 694;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_13362.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

