
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:10 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_9732.phylip" (19 taxa, 489 characters)

Minimum AIC  model: GTRI
Minimum AICc model: HKYI
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
HKYI	40	-1550.1652	3187.6519	0.3186	0.3186
HKYG	40	-1550.3378	3187.9970	0.2681	0.5867
GTRI	44	-1546.0249	3188.9688	0.1649	0.7516
GTRG	44	-1546.2828	3189.4845	0.1274	0.8791
HKYIG	41	-1550.3376	3190.3799	0.0814	0.9605
GTRIG	45	-1546.2825	3191.9103	0.0379	0.9984
K2PI	37	-1559.9244	3200.0838	0.0006	0.9990
K2PG	37	-1559.9534	3200.1418	0.0006	0.9997
K2PIG	38	-1559.9532	3202.4930	0.0002	0.9999
SYMI	41	-1557.4658	3204.6363	0.0001	0.9999
SYMG	41	-1557.5133	3204.7313	0.0001	1.0000
SYMIG	42	-1557.5130	3207.1246	0.0000	1.0000
HKY	39	-1565.5498	3216.0484	0.0000	1.0000
GTR	43	-1562.1797	3218.8629	0.0000	1.0000
K2P	36	-1574.9590	3227.8118	0.0000	1.0000
SYM	40	-1572.6459	3232.6133	0.0000	1.0000
F81I	39	-1585.0738	3255.0964	0.0000	1.0000
F81G	39	-1585.1715	3255.2918	0.0000	1.0000
F81IG	40	-1585.1712	3257.6638	0.0000	1.0000
JC69I	36	-1592.9211	3263.7361	0.0000	1.0000
JC69G	36	-1592.9546	3263.8030	0.0000	1.0000
JC69IG	37	-1592.9542	3266.1435	0.0000	1.0000
F81	38	-1599.7190	3282.0248	0.0000	1.0000
JC69	35	-1607.4681	3290.4991	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1546.0249	3180.0499	0.2545	0.2545
HKYI	40	-1550.1652	3180.3305	0.2212	0.4757
GTRG	44	-1546.2828	3180.5656	0.1966	0.6723
HKYG	40	-1550.3378	3180.6756	0.1861	0.8584
GTRIG	45	-1546.2825	3182.5650	0.0724	0.9308
HKYIG	41	-1550.3376	3182.6752	0.0685	0.9993
K2PI	37	-1559.9244	3193.8488	0.0003	0.9995
K2PG	37	-1559.9534	3193.9067	0.0002	0.9998
K2PIG	38	-1559.9532	3195.9063	0.0001	0.9999
SYMI	41	-1557.4658	3196.9316	0.0001	0.9999
SYMG	41	-1557.5133	3197.0266	0.0001	1.0000
SYMIG	42	-1557.5130	3199.0260	0.0000	1.0000
HKY	39	-1565.5498	3209.0996	0.0000	1.0000
GTR	43	-1562.1797	3210.3595	0.0000	1.0000
K2P	36	-1574.9590	3221.9180	0.0000	1.0000
SYM	40	-1572.6459	3225.2919	0.0000	1.0000
F81I	39	-1585.0738	3248.1476	0.0000	1.0000
F81G	39	-1585.1715	3248.3430	0.0000	1.0000
F81IG	40	-1585.1712	3250.3424	0.0000	1.0000
JC69I	36	-1592.9211	3257.8423	0.0000	1.0000
JC69G	36	-1592.9546	3257.9092	0.0000	1.0000
JC69IG	37	-1592.9542	3259.9085	0.0000	1.0000
F81	38	-1599.7190	3275.4381	0.0000	1.0000
JC69	35	-1607.4681	3284.9362	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1550.1652	3348.0250	0.3186	0.3186
HKYG	40	-1550.3378	3348.3701	0.2681	0.5867
K2PI	37	-1559.9244	3348.9662	0.1990	0.7857
K2PG	37	-1559.9534	3349.0241	0.1933	0.9790
HKYIG	41	-1550.3376	3354.5621	0.0121	0.9911
K2PIG	38	-1559.9532	3355.2161	0.0087	0.9998
GTRI	44	-1546.0249	3364.5138	0.0001	0.9999
GTRG	44	-1546.2828	3365.0296	0.0001	1.0000
SYMI	41	-1557.4658	3368.8184	0.0000	1.0000
SYMG	41	-1557.5133	3368.9134	0.0000	1.0000
GTRIG	45	-1546.2825	3371.2213	0.0000	1.0000
HKY	39	-1565.5498	3372.6017	0.0000	1.0000
K2P	36	-1574.9590	3372.8431	0.0000	1.0000
SYMIG	42	-1557.5130	3375.1052	0.0000	1.0000
GTR	43	-1562.1797	3390.6311	0.0000	1.0000
SYM	40	-1572.6459	3392.9864	0.0000	1.0000
JC69I	36	-1592.9211	3408.7673	0.0000	1.0000
JC69G	36	-1592.9546	3408.8343	0.0000	1.0000
F81I	39	-1585.0738	3411.6498	0.0000	1.0000
F81G	39	-1585.1715	3411.8452	0.0000	1.0000
JC69IG	37	-1592.9542	3415.0259	0.0000	1.0000
F81IG	40	-1585.1712	3418.0369	0.0000	1.0000
JC69	35	-1607.4681	3431.6688	0.0000	1.0000
F81	38	-1599.7190	3434.7479	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9732.phylip = 1 - 489;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9732.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9732.phylip = 1 - 489;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9732.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;


[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/chr3_9732.phylip = 1 - 489;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_9732.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

