
Output from mraic.pl version 1.4.4 by Johan Nylander
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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/chr2_23192.phylip" (19 taxa, 664 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	-1722.7926	3539.9826	0.4396	0.4396
GTRI	44	-1723.4790	3541.3555	0.2213	0.6608
HKYG	40	-1728.2022	3541.6692	0.1891	0.8499
HKYI	40	-1728.8190	3542.9027	0.1021	0.9520
GTRIG	45	-1724.1881	3545.0753	0.0344	0.9865
HKYIG	41	-1729.7029	3546.9427	0.0135	1.0000
GTR	43	-1741.3168	3574.7367	0.0000	1.0000
HKY	39	-1746.5678	3576.1356	0.0000	1.0000
K2PG	37	-1767.6207	3613.7334	0.0000	1.0000
K2PI	37	-1768.2542	3615.0005	0.0000	1.0000
K2PIG	38	-1767.2203	3615.1830	0.0000	1.0000
F81G	39	-1766.3051	3615.6102	0.0000	1.0000
F81I	39	-1766.8874	3616.7747	0.0000	1.0000
F81IG	40	-1766.0181	3617.3011	0.0000	1.0000
SYMG	41	-1766.7340	3621.0050	0.0000	1.0000
SYMI	41	-1767.3693	3622.2756	0.0000	1.0000
SYMIG	42	-1766.3723	3622.5611	0.0000	1.0000
F81	38	-1784.5452	3649.8329	0.0000	1.0000
K2P	36	-1786.9535	3650.1559	0.0000	1.0000
SYM	40	-1785.5798	3656.4244	0.0000	1.0000
JC69G	36	-1800.8126	3677.8739	0.0000	1.0000
JC69I	36	-1801.4171	3679.0831	0.0000	1.0000
JC69IG	37	-1800.4626	3679.4172	0.0000	1.0000
JC69	35	-1819.6496	3713.3119	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1722.7926	3533.5851	0.5024	0.5024
GTRI	44	-1723.4790	3534.9580	0.2529	0.7552
HKYG	40	-1728.2022	3536.4044	0.1227	0.8779
HKYI	40	-1728.8190	3537.6379	0.0662	0.9442
GTRIG	45	-1724.1881	3538.3762	0.0458	0.9899
HKYIG	41	-1729.7029	3541.4057	0.0101	1.0000
GTR	43	-1741.3168	3568.6335	0.0000	1.0000
HKY	39	-1746.5678	3571.1356	0.0000	1.0000
K2PG	37	-1767.6207	3609.2414	0.0000	1.0000
K2PIG	38	-1767.2203	3610.4406	0.0000	1.0000
K2PI	37	-1768.2542	3610.5085	0.0000	1.0000
F81G	39	-1766.3051	3610.6102	0.0000	1.0000
F81I	39	-1766.8874	3611.7747	0.0000	1.0000
F81IG	40	-1766.0181	3612.0363	0.0000	1.0000
SYMG	41	-1766.7340	3615.4681	0.0000	1.0000
SYMI	41	-1767.3693	3616.7386	0.0000	1.0000
SYMIG	42	-1766.3723	3616.7447	0.0000	1.0000
F81	38	-1784.5452	3645.0905	0.0000	1.0000
K2P	36	-1786.9535	3645.9071	0.0000	1.0000
SYM	40	-1785.5798	3651.1596	0.0000	1.0000
JC69G	36	-1800.8126	3673.6251	0.0000	1.0000
JC69I	36	-1801.4171	3674.8343	0.0000	1.0000
JC69IG	37	-1800.4626	3674.9252	0.0000	1.0000
JC69	35	-1819.6496	3709.2992	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1728.2022	3716.3356	0.6455	0.6455
HKYI	40	-1728.8190	3717.5692	0.3484	0.9939
HKYIG	41	-1729.7029	3725.8353	0.0056	0.9995
GTRG	44	-1722.7926	3731.5096	0.0003	0.9998
GTRI	44	-1723.4790	3732.8825	0.0002	1.0000
GTRIG	45	-1724.1881	3740.7989	0.0000	1.0000
HKY	39	-1746.5678	3746.5686	0.0000	1.0000
GTR	43	-1741.3168	3762.0597	0.0000	1.0000
K2PG	37	-1767.6207	3775.6778	0.0000	1.0000
K2PI	37	-1768.2542	3776.9449	0.0000	1.0000
K2PIG	38	-1767.2203	3781.3753	0.0000	1.0000
F81G	39	-1766.3051	3786.0432	0.0000	1.0000
F81I	39	-1766.8874	3787.2077	0.0000	1.0000
F81IG	40	-1766.0181	3791.9675	0.0000	1.0000
SYMG	41	-1766.7340	3799.8976	0.0000	1.0000
SYMI	41	-1767.3693	3801.1682	0.0000	1.0000
SYMIG	42	-1766.3723	3805.6725	0.0000	1.0000
K2P	36	-1786.9535	3807.8453	0.0000	1.0000
F81	38	-1784.5452	3816.0252	0.0000	1.0000
SYM	40	-1785.5798	3831.0908	0.0000	1.0000
JC69G	36	-1800.8126	3835.5633	0.0000	1.0000
JC69I	36	-1801.4171	3836.7724	0.0000	1.0000
JC69IG	37	-1800.4626	3841.3616	0.0000	1.0000
JC69	35	-1819.6496	3866.7390	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/chr2_23192.phylip = 1 - 664;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23192.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/chr2_23192.phylip = 1 - 664;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23192.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/chr2_23192.phylip = 1 - 664;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23192.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

