
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:06 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/chr7_4674.phylip" (19 taxa, 672 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1562.7728	3219.8613	0.4359	0.4359
GTRI	44	-1562.9702	3220.2562	0.3578	0.7938
GTRIG	45	-1562.5712	3221.7558	0.1691	0.9628
HKYI	40	-1570.6244	3226.4469	0.0162	0.9790
HKYG	40	-1570.6527	3226.5036	0.0157	0.9948
HKYIG	41	-1570.6525	3228.7717	0.0051	0.9998
SYMG	41	-1575.2397	3237.9461	0.0001	0.9999
SYMI	41	-1575.3029	3238.0724	0.0000	0.9999
SYMIG	42	-1575.1562	3240.0549	0.0000	1.0000
K2PI	37	-1580.9600	3240.3554	0.0000	1.0000
K2PG	37	-1580.9606	3240.3565	0.0000	1.0000
K2PIG	38	-1580.9497	3242.5818	0.0000	1.0000
GTR	43	-1580.0151	3252.0557	0.0000	1.0000
HKY	39	-1591.2102	3265.3570	0.0000	1.0000
F81G	39	-1592.4881	3267.9129	0.0000	1.0000
F81I	39	-1592.4933	3267.9234	0.0000	1.0000
F81IG	40	-1592.4888	3270.1756	0.0000	1.0000
SYM	40	-1594.2123	3273.6227	0.0000	1.0000
JC69G	36	-1600.8121	3277.8196	0.0000	1.0000
JC69I	36	-1600.8154	3277.8261	0.0000	1.0000
JC69IG	37	-1600.8093	3280.0540	0.0000	1.0000
K2P	36	-1603.0917	3282.3788	0.0000	1.0000
F81	38	-1612.8201	3306.3226	0.0000	1.0000
JC69	35	-1621.9797	3317.9217	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1562.7728	3213.5455	0.4309	0.4309
GTRI	44	-1562.9702	3213.9404	0.3537	0.7846
GTRIG	45	-1562.5712	3215.1424	0.1939	0.9786
HKYI	40	-1570.6244	3221.2488	0.0092	0.9877
HKYG	40	-1570.6527	3221.3055	0.0089	0.9966
HKYIG	41	-1570.6525	3223.3051	0.0033	0.9999
SYMG	41	-1575.2397	3232.4794	0.0000	0.9999
SYMI	41	-1575.3029	3232.6057	0.0000	1.0000
SYMIG	42	-1575.1562	3234.3125	0.0000	1.0000
K2PI	37	-1580.9600	3235.9200	0.0000	1.0000
K2PG	37	-1580.9606	3235.9212	0.0000	1.0000
K2PIG	38	-1580.9497	3237.8994	0.0000	1.0000
GTR	43	-1580.0151	3246.0302	0.0000	1.0000
HKY	39	-1591.2102	3260.4203	0.0000	1.0000
F81G	39	-1592.4881	3262.9762	0.0000	1.0000
F81I	39	-1592.4933	3262.9867	0.0000	1.0000
F81IG	40	-1592.4888	3264.9775	0.0000	1.0000
SYM	40	-1594.2123	3268.4246	0.0000	1.0000
JC69G	36	-1600.8121	3273.6243	0.0000	1.0000
JC69I	36	-1600.8154	3273.6308	0.0000	1.0000
JC69IG	37	-1600.8093	3275.6187	0.0000	1.0000
K2P	36	-1603.0917	3278.1835	0.0000	1.0000
F81	38	-1612.8201	3301.6402	0.0000	1.0000
JC69	35	-1621.9797	3313.9594	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1570.6244	3401.6591	0.3151	0.3151
HKYG	40	-1570.6527	3401.7158	0.3063	0.6214
K2PI	37	-1580.9600	3402.7996	0.1782	0.7996
K2PG	37	-1580.9606	3402.8008	0.1781	0.9776
HKYIG	41	-1570.6525	3408.2257	0.0118	0.9895
K2PIG	38	-1580.9497	3409.2892	0.0069	0.9964
GTRG	44	-1562.7728	3411.9969	0.0018	0.9982
GTRI	44	-1562.9702	3412.3918	0.0015	0.9997
SYMG	41	-1575.2397	3417.4000	0.0001	0.9998
SYMI	41	-1575.3029	3417.5263	0.0001	0.9999
GTRIG	45	-1562.5712	3418.1040	0.0001	1.0000
SYMIG	42	-1575.1562	3423.7434	0.0000	1.0000
JC69G	36	-1600.8121	3435.9936	0.0000	1.0000
JC69I	36	-1600.8154	3436.0001	0.0000	1.0000
HKY	39	-1591.2102	3436.3204	0.0000	1.0000
F81G	39	-1592.4881	3438.8763	0.0000	1.0000
F81I	39	-1592.4933	3438.8868	0.0000	1.0000
GTR	43	-1580.0151	3439.9713	0.0000	1.0000
K2P	36	-1603.0917	3440.5528	0.0000	1.0000
JC69IG	37	-1600.8093	3442.4983	0.0000	1.0000
F81IG	40	-1592.4888	3445.3879	0.0000	1.0000
SYM	40	-1594.2123	3448.8350	0.0000	1.0000
JC69	35	-1621.9797	3471.8185	0.0000	1.0000
F81	38	-1612.8201	3473.0300	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/chr7_4674.phylip = 1 - 672;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4674.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/chr7_4674.phylip = 1 - 672;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4674.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4674.phylip = 1 - 672;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4674.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

