
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:15 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_5450.phylip" (19 taxa, 543 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	-1868.7015	3833.3547	0.6321	0.6321
GTRIG	45	-1868.6834	3835.6968	0.1960	0.8281
GTRI	44	-1870.0638	3836.0795	0.1619	0.9900
SYMG	41	-1877.6626	3844.1994	0.0028	0.9928
HKYG	40	-1878.9211	3844.3760	0.0026	0.9954
HKYI	40	-1879.5811	3845.6961	0.0013	0.9967
SYMI	41	-1878.6030	3846.0802	0.0011	0.9978
SYMIG	42	-1877.6331	3846.4903	0.0009	0.9987
HKYIG	41	-1878.8925	3846.6593	0.0008	0.9995
K2PG	37	-1884.6445	3848.8572	0.0003	0.9997
K2PI	37	-1885.1217	3849.8118	0.0002	0.9999
K2PIG	38	-1884.5913	3851.0635	0.0001	1.0000
GTR	43	-1885.6429	3864.8690	0.0000	1.0000
HKY	39	-1895.9511	3876.1050	0.0000	1.0000
SYM	40	-1894.8347	3876.2032	0.0000	1.0000
K2P	36	-1902.2699	3881.8046	0.0000	1.0000
F81G	39	-1921.6744	3927.5517	0.0000	1.0000
F81I	39	-1922.0077	3928.2181	0.0000	1.0000
F81IG	40	-1921.6429	3929.8197	0.0000	1.0000
JC69G	36	-1926.9672	3931.1992	0.0000	1.0000
JC69I	36	-1927.2593	3931.7833	0.0000	1.0000
JC69IG	37	-1926.9188	3933.4058	0.0000	1.0000
F81	38	-1937.8341	3957.5491	0.0000	1.0000
JC69	35	-1943.6403	3962.2511	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1868.7015	3825.4029	0.6100	0.6100
GTRIG	45	-1868.6834	3827.3668	0.2285	0.8386
GTRI	44	-1870.0638	3828.1277	0.1562	0.9948
SYMG	41	-1877.6626	3837.3251	0.0016	0.9963
HKYG	40	-1878.9211	3837.8421	0.0012	0.9975
HKYI	40	-1879.5811	3839.1622	0.0006	0.9982
SYMI	41	-1878.6030	3839.2060	0.0006	0.9988
SYMIG	42	-1877.6331	3839.2663	0.0006	0.9994
HKYIG	41	-1878.8925	3839.7850	0.0005	0.9998
K2PG	37	-1884.6445	3843.2889	0.0001	0.9999
K2PI	37	-1885.1217	3844.2435	0.0000	1.0000
K2PIG	38	-1884.5913	3845.1825	0.0000	1.0000
GTR	43	-1885.6429	3857.2859	0.0000	1.0000
SYM	40	-1894.8347	3869.6693	0.0000	1.0000
HKY	39	-1895.9511	3869.9023	0.0000	1.0000
K2P	36	-1902.2699	3876.5398	0.0000	1.0000
F81G	39	-1921.6744	3921.3489	0.0000	1.0000
F81I	39	-1922.0077	3922.0153	0.0000	1.0000
F81IG	40	-1921.6429	3923.2858	0.0000	1.0000
JC69G	36	-1926.9672	3925.9344	0.0000	1.0000
JC69I	36	-1927.2593	3926.5185	0.0000	1.0000
JC69IG	37	-1926.9188	3927.8375	0.0000	1.0000
F81	38	-1937.8341	3951.6682	0.0000	1.0000
JC69	35	-1943.6403	3957.2807	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1884.6445	4002.2819	0.5842	0.5842
K2PI	37	-1885.1217	4003.2365	0.3625	0.9467
K2PIG	38	-1884.5913	4008.4727	0.0264	0.9732
HKYG	40	-1878.9211	4009.7265	0.0141	0.9873
HKYI	40	-1879.5811	4011.0466	0.0073	0.9946
SYMG	41	-1877.6626	4013.5066	0.0021	0.9967
GTRG	44	-1868.7015	4014.4758	0.0013	0.9981
SYMI	41	-1878.6030	4015.3874	0.0008	0.9989
HKYIG	41	-1878.8925	4015.9665	0.0006	0.9995
GTRI	44	-1870.0638	4017.2005	0.0003	0.9998
SYMIG	42	-1877.6331	4019.7449	0.0001	0.9999
GTRIG	45	-1868.6834	4020.7367	0.0001	1.0000
K2P	36	-1902.2699	4031.2357	0.0000	1.0000
HKY	39	-1895.9511	4037.4895	0.0000	1.0000
SYM	40	-1894.8347	4041.5537	0.0000	1.0000
GTR	43	-1885.6429	4042.0616	0.0000	1.0000
JC69G	36	-1926.9672	4080.6304	0.0000	1.0000
JC69I	36	-1927.2593	4081.2145	0.0000	1.0000
JC69IG	37	-1926.9188	4086.8305	0.0000	1.0000
F81G	39	-1921.6744	4088.9362	0.0000	1.0000
F81I	39	-1922.0077	4089.6026	0.0000	1.0000
F81IG	40	-1921.6429	4095.1702	0.0000	1.0000
JC69	35	-1943.6403	4107.6795	0.0000	1.0000
F81	38	-1937.8341	4114.9583	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_5450.phylip = 1 - 543;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5450.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_5450.phylip = 1 - 543;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5450.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_5450.phylip = 1 - 543;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5450.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

