
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:50 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_25941.phylip" (19 taxa, 524 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	-2103.5907	4303.4487	0.5123	0.5123
HKYG	40	-2109.0432	4304.8772	0.2508	0.7632
GTRIG	45	-2103.5878	4305.8367	0.1552	0.9184
HKYIG	41	-2109.0406	4307.2263	0.0775	0.9959
HKYI	40	-2113.7123	4314.2154	0.0024	0.9982
GTRI	44	-2109.2672	4314.8016	0.0018	1.0000
K2PG	37	-2142.7493	4365.2846	0.0000	1.0000
K2PIG	38	-2142.7340	4367.5793	0.0000	1.0000
SYMG	41	-2143.6741	4376.4934	0.0000	1.0000
K2PI	37	-2149.1058	4377.9976	0.0000	1.0000
SYMIG	42	-2143.6152	4378.7397	0.0000	1.0000
SYMI	41	-2148.5858	4386.3169	0.0000	1.0000
F81G	39	-2154.5091	4393.4645	0.0000	1.0000
F81IG	40	-2154.4494	4395.6898	0.0000	1.0000
GTR	43	-2150.9339	4395.7512	0.0000	1.0000
F81I	39	-2159.8883	4404.2229	0.0000	1.0000
HKY	39	-2161.7696	4407.9855	0.0000	1.0000
JC69G	36	-2182.2277	4441.9257	0.0000	1.0000
JC69IG	37	-2182.1558	4444.0976	0.0000	1.0000
JC69I	36	-2187.5383	4452.5467	0.0000	1.0000
K2P	36	-2198.9081	4475.2864	0.0000	1.0000
SYM	40	-2196.9913	4480.7734	0.0000	1.0000
F81	38	-2204.3219	4490.7552	0.0000	1.0000
JC69	35	-2232.6733	4540.5105	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2103.5907	4295.1815	0.5900	0.5900
GTRIG	45	-2103.5878	4297.1756	0.2177	0.8077
HKYG	40	-2109.0432	4298.0863	0.1381	0.9458
HKYIG	41	-2109.0406	4300.0811	0.0509	0.9967
GTRI	44	-2109.2672	4306.5344	0.0020	0.9987
HKYI	40	-2113.7123	4307.4245	0.0013	1.0000
K2PG	37	-2142.7493	4359.4986	0.0000	1.0000
K2PIG	38	-2142.7340	4361.4680	0.0000	1.0000
SYMG	41	-2143.6741	4369.3482	0.0000	1.0000
SYMIG	42	-2143.6152	4371.2303	0.0000	1.0000
K2PI	37	-2149.1058	4372.2116	0.0000	1.0000
SYMI	41	-2148.5858	4379.1717	0.0000	1.0000
F81G	39	-2154.5091	4387.0182	0.0000	1.0000
GTR	43	-2150.9339	4387.8679	0.0000	1.0000
F81IG	40	-2154.4494	4388.8989	0.0000	1.0000
F81I	39	-2159.8883	4397.7766	0.0000	1.0000
HKY	39	-2161.7696	4401.5392	0.0000	1.0000
JC69G	36	-2182.2277	4436.4554	0.0000	1.0000
JC69IG	37	-2182.1558	4438.3116	0.0000	1.0000
JC69I	36	-2187.5383	4447.0765	0.0000	1.0000
K2P	36	-2198.9081	4469.8161	0.0000	1.0000
SYM	40	-2196.9913	4473.9825	0.0000	1.0000
F81	38	-2204.3219	4484.6439	0.0000	1.0000
JC69	35	-2232.6733	4535.3465	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2109.0432	4468.5460	0.9487	0.9487
HKYIG	41	-2109.0406	4474.8023	0.0416	0.9903
HKYI	40	-2113.7123	4477.8842	0.0089	0.9992
GTRG	44	-2103.5907	4482.6871	0.0008	1.0000
GTRIG	45	-2103.5878	4488.9428	0.0000	1.0000
GTRI	44	-2109.2672	4494.0401	0.0000	1.0000
K2PG	37	-2142.7493	4517.1738	0.0000	1.0000
K2PIG	38	-2142.7340	4523.4047	0.0000	1.0000
K2PI	37	-2149.1058	4529.8868	0.0000	1.0000
SYMG	41	-2143.6741	4544.0693	0.0000	1.0000
SYMIG	42	-2143.6152	4550.2130	0.0000	1.0000
F81G	39	-2154.5091	4553.2164	0.0000	1.0000
SYMI	41	-2148.5858	4553.8928	0.0000	1.0000
F81IG	40	-2154.4494	4559.3585	0.0000	1.0000
F81I	39	-2159.8883	4563.9748	0.0000	1.0000
HKY	39	-2161.7696	4567.7374	0.0000	1.0000
GTR	43	-2150.9339	4571.1120	0.0000	1.0000
JC69G	36	-2182.2277	4589.8691	0.0000	1.0000
JC69IG	37	-2182.1558	4595.9868	0.0000	1.0000
JC69I	36	-2187.5383	4600.4902	0.0000	1.0000
K2P	36	-2198.9081	4623.2298	0.0000	1.0000
SYM	40	-2196.9913	4644.4422	0.0000	1.0000
F81	38	-2204.3219	4646.5805	0.0000	1.0000
JC69	35	-2232.6733	4684.4987	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_25941.phylip = 1 - 524;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25941.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_25941.phylip = 1 - 524;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25941.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_25941.phylip = 1 - 524;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25941.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

