
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:20 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/chr3_1249.phylip" (19 taxa, 428 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-1541.9232	3182.1857	0.6998	0.6998
GTRIG	45	-1541.7393	3184.3163	0.2412	0.9410
GTRI	44	-1544.6093	3187.5580	0.0477	0.9887
HKYG	40	-1551.4402	3191.3559	0.0071	0.9958
HKYIG	41	-1551.2629	3193.4481	0.0025	0.9983
HKYI	40	-1553.9641	3196.4037	0.0006	0.9989
SYMG	41	-1552.9395	3196.8013	0.0005	0.9994
K2PG	37	-1558.2494	3197.7091	0.0003	0.9997
SYMIG	42	-1552.7292	3198.8402	0.0002	0.9998
K2PIG	38	-1558.0542	3199.7280	0.0001	0.9999
SYMI	41	-1555.3666	3201.6555	0.0000	1.0000
K2PI	37	-1560.9094	3203.0291	0.0000	1.0000
GTR	43	-1561.6159	3219.0859	0.0000	1.0000
HKY	39	-1571.1068	3228.2548	0.0000	1.0000
SYM	40	-1573.1925	3234.8605	0.0000	1.0000
K2P	36	-1578.9910	3236.7953	0.0000	1.0000
F81G	39	-1609.4145	3304.8703	0.0000	1.0000
F81IG	40	-1609.4534	3307.3822	0.0000	1.0000
JC69G	36	-1614.7498	3308.3129	0.0000	1.0000
F81I	39	-1611.6482	3309.3377	0.0000	1.0000
JC69IG	37	-1614.3840	3309.9782	0.0000	1.0000
JC69I	36	-1616.6208	3312.0549	0.0000	1.0000
F81	38	-1628.2539	3340.1274	0.0000	1.0000
JC69	35	-1634.0277	3344.4841	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1541.9232	3171.8463	0.6592	0.6592
GTRIG	45	-1541.7393	3173.4786	0.2915	0.9506
GTRI	44	-1544.6093	3177.2186	0.0449	0.9956
HKYG	40	-1551.4402	3182.8805	0.0026	0.9982
HKYIG	41	-1551.2629	3184.5259	0.0012	0.9994
SYMG	41	-1552.9395	3187.8790	0.0002	0.9996
HKYI	40	-1553.9641	3187.9283	0.0002	0.9998
SYMIG	42	-1552.7292	3189.4583	0.0001	0.9999
K2PG	37	-1558.2494	3190.4988	0.0001	1.0000
K2PIG	38	-1558.0542	3192.1084	0.0000	1.0000
SYMI	41	-1555.3666	3192.7332	0.0000	1.0000
K2PI	37	-1560.9094	3195.8188	0.0000	1.0000
GTR	43	-1561.6159	3209.2318	0.0000	1.0000
HKY	39	-1571.1068	3220.2136	0.0000	1.0000
SYM	40	-1573.1925	3226.3850	0.0000	1.0000
K2P	36	-1578.9910	3229.9820	0.0000	1.0000
F81G	39	-1609.4145	3296.8290	0.0000	1.0000
F81IG	40	-1609.4534	3298.9068	0.0000	1.0000
F81I	39	-1611.6482	3301.2965	0.0000	1.0000
JC69G	36	-1614.7498	3301.4996	0.0000	1.0000
JC69IG	37	-1614.3840	3302.7680	0.0000	1.0000
JC69I	36	-1616.6208	3305.2416	0.0000	1.0000
F81	38	-1628.2539	3332.5078	0.0000	1.0000
JC69	35	-1634.0277	3338.0555	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1558.2494	3340.6864	0.7968	0.7968
HKYG	40	-1551.4402	3345.2454	0.0815	0.8784
K2PI	37	-1560.9094	3346.0064	0.0557	0.9341
K2PIG	38	-1558.0542	3346.3551	0.0468	0.9809
HKYI	40	-1553.9641	3350.2932	0.0065	0.9875
GTRG	44	-1541.9232	3350.4477	0.0060	0.9935
HKYIG	41	-1551.2629	3350.9499	0.0047	0.9982
SYMG	41	-1552.9395	3354.3031	0.0009	0.9991
GTRI	44	-1544.6093	3355.8200	0.0004	0.9995
GTRIG	45	-1541.7393	3356.1391	0.0004	0.9999
SYMI	41	-1555.3666	3359.1573	0.0001	0.9999
SYMIG	42	-1552.7292	3359.9415	0.0001	1.0000
K2P	36	-1578.9910	3376.1105	0.0000	1.0000
HKY	39	-1571.1068	3378.5194	0.0000	1.0000
GTR	43	-1561.6159	3383.7741	0.0000	1.0000
SYM	40	-1573.1925	3388.7499	0.0000	1.0000
JC69G	36	-1614.7498	3447.6280	0.0000	1.0000
JC69I	36	-1616.6208	3451.3700	0.0000	1.0000
JC69IG	37	-1614.3840	3452.9555	0.0000	1.0000
F81G	39	-1609.4145	3455.1348	0.0000	1.0000
F81I	39	-1611.6482	3459.6023	0.0000	1.0000
F81IG	40	-1609.4534	3461.2717	0.0000	1.0000
JC69	35	-1634.0277	3480.1248	0.0000	1.0000
F81	38	-1628.2539	3486.7545	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/chr3_1249.phylip = 1 - 428;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1249.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/chr3_1249.phylip = 1 - 428;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1249.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1249.phylip = 1 - 428;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_1249.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

