
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:07 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/chr9_7170.phylip" (19 taxa, 571 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	-1515.3419	3126.2124	0.4754	0.4754
GTRI	44	-1515.8159	3127.1603	0.2960	0.7714
GTRIG	45	-1514.9008	3127.6873	0.2274	0.9988
HKYG	40	-1526.7127	3139.6141	0.0006	0.9994
HKYI	40	-1527.1265	3140.4416	0.0004	0.9997
HKYIG	41	-1526.3797	3141.2699	0.0003	1.0000
SYMG	41	-1541.3762	3171.2628	0.0000	1.0000
SYMI	41	-1541.8977	3172.3059	0.0000	1.0000
SYMIG	42	-1540.8842	3172.6092	0.0000	1.0000
K2PG	37	-1547.1805	3173.6368	0.0000	1.0000
K2PI	37	-1547.6682	3174.6122	0.0000	1.0000
K2PIG	38	-1546.7766	3175.1246	0.0000	1.0000
GTR	43	-1541.2742	3175.7286	0.0000	1.0000
HKY	39	-1551.2640	3186.4037	0.0000	1.0000
F81G	39	-1557.9486	3199.7729	0.0000	1.0000
F81I	39	-1558.4735	3200.8228	0.0000	1.0000
F81IG	40	-1557.6115	3201.4117	0.0000	1.0000
SYM	40	-1565.1852	3216.5591	0.0000	1.0000
K2P	36	-1570.9670	3218.9227	0.0000	1.0000
JC69G	36	-1574.5979	3226.1846	0.0000	1.0000
JC69I	36	-1575.1308	3227.2503	0.0000	1.0000
JC69IG	37	-1574.2429	3227.7617	0.0000	1.0000
F81	38	-1580.8445	3243.2605	0.0000	1.0000
JC69	35	-1597.3924	3269.4950	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1515.3419	3118.6839	0.4554	0.4554
GTRI	44	-1515.8159	3119.6318	0.2835	0.7389
GTRIG	45	-1514.9008	3119.8016	0.2604	0.9994
HKYG	40	-1526.7127	3133.4255	0.0003	0.9997
HKYI	40	-1527.1265	3134.2529	0.0002	0.9999
HKYIG	41	-1526.3797	3134.7595	0.0001	1.0000
SYMG	41	-1541.3762	3164.7524	0.0000	1.0000
SYMIG	42	-1540.8842	3165.7683	0.0000	1.0000
SYMI	41	-1541.8977	3165.7955	0.0000	1.0000
K2PG	37	-1547.1805	3168.3610	0.0000	1.0000
GTR	43	-1541.2742	3168.5484	0.0000	1.0000
K2PI	37	-1547.6682	3169.3364	0.0000	1.0000
K2PIG	38	-1546.7766	3169.5531	0.0000	1.0000
HKY	39	-1551.2640	3180.5280	0.0000	1.0000
F81G	39	-1557.9486	3193.8972	0.0000	1.0000
F81I	39	-1558.4735	3194.9471	0.0000	1.0000
F81IG	40	-1557.6115	3195.2230	0.0000	1.0000
SYM	40	-1565.1852	3210.3704	0.0000	1.0000
K2P	36	-1570.9670	3213.9339	0.0000	1.0000
JC69G	36	-1574.5979	3221.1958	0.0000	1.0000
JC69I	36	-1575.1308	3222.2615	0.0000	1.0000
JC69IG	37	-1574.2429	3222.4859	0.0000	1.0000
F81	38	-1580.8445	3237.6891	0.0000	1.0000
JC69	35	-1597.3924	3264.7847	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1526.7127	3307.3210	0.4611	0.4611
HKYI	40	-1527.1265	3308.1485	0.3049	0.7660
GTRG	44	-1515.3419	3309.9690	0.1227	0.8887
GTRI	44	-1515.8159	3310.9169	0.0764	0.9651
HKYIG	41	-1526.3797	3313.0024	0.0269	0.9920
GTRIG	45	-1514.9008	3315.4341	0.0080	1.0000
K2PG	37	-1547.1805	3329.2144	0.0000	1.0000
K2PI	37	-1547.6682	3330.1898	0.0000	1.0000
K2PIG	38	-1546.7766	3334.7539	0.0000	1.0000
SYMG	41	-1541.3762	3342.9954	0.0000	1.0000
SYMI	41	-1541.8977	3344.0384	0.0000	1.0000
SYMIG	42	-1540.8842	3348.3587	0.0000	1.0000
HKY	39	-1551.2640	3350.0762	0.0000	1.0000
GTR	43	-1541.2742	3355.4861	0.0000	1.0000
F81G	39	-1557.9486	3363.4453	0.0000	1.0000
F81I	39	-1558.4735	3364.4953	0.0000	1.0000
F81IG	40	-1557.6115	3369.1186	0.0000	1.0000
K2P	36	-1570.9670	3370.4399	0.0000	1.0000
JC69G	36	-1574.5979	3377.7018	0.0000	1.0000
JC69I	36	-1575.1308	3378.7675	0.0000	1.0000
JC69IG	37	-1574.2429	3383.3393	0.0000	1.0000
SYM	40	-1565.1852	3384.2660	0.0000	1.0000
F81	38	-1580.8445	3402.8898	0.0000	1.0000
JC69	35	-1597.3924	3416.9434	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/chr9_7170.phylip = 1 - 571;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7170.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/chr9_7170.phylip = 1 - 571;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7170.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/chr9_7170.phylip = 1 - 571;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7170.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

