
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:52 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_2740.phylip" (19 taxa, 572 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	-1607.2819	3310.0780	0.4469	0.4469
GTRI	44	-1607.3990	3310.3123	0.3975	0.8444
GTRIG	45	-1607.2931	3312.4570	0.1360	0.9805
GTR	43	-1612.2019	3317.5705	0.0105	0.9910
HKYG	40	-1616.5963	3319.3696	0.0043	0.9953
HKYI	40	-1616.8652	3319.9074	0.0033	0.9986
HKYIG	41	-1616.6124	3321.7229	0.0013	0.9999
HKY	39	-1621.6575	3327.1797	0.0001	1.0000
SYMG	41	-1622.6625	3333.8231	0.0000	1.0000
SYMI	41	-1622.7891	3334.0763	0.0000	1.0000
SYMIG	42	-1622.6730	3336.1741	0.0000	1.0000
K2PG	37	-1631.0436	3341.3530	0.0000	1.0000
SYM	40	-1627.8291	3341.8352	0.0000	1.0000
K2PI	37	-1631.2986	3341.8632	0.0000	1.0000
K2PIG	38	-1631.0578	3343.6766	0.0000	1.0000
K2P	36	-1636.3075	3349.5945	0.0000	1.0000
F81G	39	-1633.2332	3350.3311	0.0000	1.0000
F81I	39	-1633.4616	3350.7878	0.0000	1.0000
F81IG	40	-1633.2509	3352.6788	0.0000	1.0000
F81	38	-1638.1282	3357.8173	0.0000	1.0000
JC69G	36	-1646.4055	3369.7905	0.0000	1.0000
JC69I	36	-1646.6240	3370.2275	0.0000	1.0000
JC69IG	37	-1646.4221	3372.1102	0.0000	1.0000
JC69	35	-1651.4287	3377.5588	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1607.2819	3302.5637	0.4379	0.4379
GTRI	44	-1607.3990	3302.7981	0.3895	0.8274
GTRIG	45	-1607.2931	3304.5862	0.1593	0.9867
GTR	43	-1612.2019	3310.4039	0.0087	0.9954
HKYG	40	-1616.5963	3313.1926	0.0022	0.9975
HKYI	40	-1616.8652	3313.7303	0.0016	0.9992
HKYIG	41	-1616.6124	3315.2248	0.0008	1.0000
HKY	39	-1621.6575	3321.3151	0.0000	1.0000
SYMG	41	-1622.6625	3327.3250	0.0000	1.0000
SYMI	41	-1622.7891	3327.5782	0.0000	1.0000
SYMIG	42	-1622.6730	3329.3461	0.0000	1.0000
SYM	40	-1627.8291	3335.6582	0.0000	1.0000
K2PG	37	-1631.0436	3336.0871	0.0000	1.0000
K2PI	37	-1631.2986	3336.5973	0.0000	1.0000
K2PIG	38	-1631.0578	3338.1156	0.0000	1.0000
F81G	39	-1633.2332	3344.4664	0.0000	1.0000
K2P	36	-1636.3075	3344.6150	0.0000	1.0000
F81I	39	-1633.4616	3344.9231	0.0000	1.0000
F81IG	40	-1633.2509	3346.5018	0.0000	1.0000
F81	38	-1638.1282	3352.2563	0.0000	1.0000
JC69G	36	-1646.4055	3364.8110	0.0000	1.0000
JC69I	36	-1646.6240	3365.2481	0.0000	1.0000
JC69IG	37	-1646.4221	3366.8443	0.0000	1.0000
JC69	35	-1651.4287	3372.8573	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1616.5963	3487.1581	0.4896	0.4896
HKYI	40	-1616.8652	3487.6959	0.3741	0.8637
HKY	39	-1621.6575	3490.9315	0.0742	0.9379
HKYIG	41	-1616.6124	3493.5395	0.0201	0.9580
GTRG	44	-1607.2819	3493.9259	0.0166	0.9746
GTRI	44	-1607.3990	3494.1602	0.0148	0.9894
K2PG	37	-1631.0436	3497.0053	0.0036	0.9930
GTR	43	-1612.2019	3497.4168	0.0029	0.9959
K2PI	37	-1631.2986	3497.5154	0.0028	0.9986
GTRIG	45	-1607.2931	3500.2975	0.0007	0.9993
K2P	36	-1636.3075	3501.1840	0.0004	0.9998
K2PIG	38	-1631.0578	3503.3829	0.0001	0.9999
SYMG	41	-1622.6625	3505.6397	0.0000	0.9999
SYMI	41	-1622.7891	3505.8929	0.0000	1.0000
SYM	40	-1627.8291	3509.6237	0.0000	1.0000
SYMIG	42	-1622.6730	3512.0099	0.0000	1.0000
F81G	39	-1633.2332	3514.0829	0.0000	1.0000
F81I	39	-1633.4616	3514.5396	0.0000	1.0000
F81	38	-1638.1282	3517.5236	0.0000	1.0000
F81IG	40	-1633.2509	3520.4673	0.0000	1.0000
JC69G	36	-1646.4055	3521.3800	0.0000	1.0000
JC69I	36	-1646.6240	3521.8171	0.0000	1.0000
JC69	35	-1651.4287	3525.0772	0.0000	1.0000
JC69IG	37	-1646.4221	3527.7624	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_2740.phylip = 1 - 572;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2740.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_2740.phylip = 1 - 572;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2740.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/chr3_2740.phylip = 1 - 572;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2740.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

