
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:24 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/chrZ_11569.phylip" (19 taxa, 603 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1908.4170	3902.6703	0.4341	0.4341
HKYIG	41	-1907.8503	3903.8397	0.2419	0.6760
GTRG	44	-1904.5976	3904.2921	0.1929	0.8689
GTRIG	45	-1904.0791	3905.5908	0.1008	0.9697
HKYI	40	-1911.5226	3908.8815	0.0194	0.9892
GTRI	44	-1907.4813	3910.0593	0.0108	1.0000
K2PG	37	-1921.9376	3922.8523	0.0000	1.0000
K2PIG	38	-1921.3170	3923.8893	0.0000	1.0000
SYMG	41	-1920.2734	3928.6858	0.0000	1.0000
K2PI	37	-1925.1839	3929.3448	0.0000	1.0000
SYMIG	42	-1919.5989	3929.6478	0.0000	1.0000
SYMI	41	-1923.2024	3934.5439	0.0000	1.0000
HKY	39	-1935.1029	3953.7475	0.0000	1.0000
GTR	43	-1930.9985	3954.7661	0.0000	1.0000
K2P	36	-1949.9178	3976.5424	0.0000	1.0000
SYM	40	-1948.2254	3982.2871	0.0000	1.0000
F81G	39	-1951.6325	3986.8067	0.0000	1.0000
F81IG	40	-1951.1439	3988.1241	0.0000	1.0000
F81I	39	-1955.1064	3993.7545	0.0000	1.0000
JC69G	36	-1963.6120	4003.9307	0.0000	1.0000
JC69IG	37	-1963.0544	4005.0857	0.0000	1.0000
JC69I	36	-1967.1181	4010.9429	0.0000	1.0000
F81	38	-1976.5042	4034.2638	0.0000	1.0000
JC69	35	-1989.4999	4053.4443	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1908.4170	3896.8340	0.3236	0.3236
GTRG	44	-1904.5976	3897.1953	0.2701	0.5937
HKYIG	41	-1907.8503	3897.7007	0.2098	0.8035
GTRIG	45	-1904.0791	3898.1581	0.1669	0.9704
GTRI	44	-1907.4813	3902.9625	0.0151	0.9855
HKYI	40	-1911.5226	3903.0452	0.0145	1.0000
K2PG	37	-1921.9376	3917.8753	0.0000	1.0000
K2PIG	38	-1921.3170	3918.6340	0.0000	1.0000
SYMG	41	-1920.2734	3922.5467	0.0000	1.0000
SYMIG	42	-1919.5989	3923.1978	0.0000	1.0000
K2PI	37	-1925.1839	3924.3678	0.0000	1.0000
SYMI	41	-1923.2024	3928.4049	0.0000	1.0000
GTR	43	-1930.9985	3947.9969	0.0000	1.0000
HKY	39	-1935.1029	3948.2058	0.0000	1.0000
K2P	36	-1949.9178	3971.8356	0.0000	1.0000
SYM	40	-1948.2254	3976.4508	0.0000	1.0000
F81G	39	-1951.6325	3981.2650	0.0000	1.0000
F81IG	40	-1951.1439	3982.2878	0.0000	1.0000
F81I	39	-1955.1064	3988.2128	0.0000	1.0000
JC69G	36	-1963.6120	3999.2240	0.0000	1.0000
JC69IG	37	-1963.0544	4000.1087	0.0000	1.0000
JC69I	36	-1967.1181	4006.2362	0.0000	1.0000
F81	38	-1976.5042	4029.0085	0.0000	1.0000
JC69	35	-1989.4999	4048.9998	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1908.4170	4072.9107	0.8781	0.8781
HKYIG	41	-1907.8503	4078.1793	0.0630	0.9411
HKYI	40	-1911.5226	4079.1218	0.0393	0.9804
K2PG	37	-1921.9376	4080.7462	0.0175	0.9979
K2PIG	38	-1921.3170	4085.9069	0.0013	0.9992
K2PI	37	-1925.1839	4087.2387	0.0007	0.9999
GTRG	44	-1904.5976	4090.8796	0.0001	1.0000
GTRIG	45	-1904.0791	4096.2444	0.0000	1.0000
GTRI	44	-1907.4813	4096.6469	0.0000	1.0000
SYMG	41	-1920.2734	4103.0253	0.0000	1.0000
SYMIG	42	-1919.5989	4108.0783	0.0000	1.0000
SYMI	41	-1923.2024	4108.8835	0.0000	1.0000
HKY	39	-1935.1029	4119.8806	0.0000	1.0000
K2P	36	-1949.9178	4130.3047	0.0000	1.0000
GTR	43	-1930.9985	4137.2793	0.0000	1.0000
SYM	40	-1948.2254	4152.5274	0.0000	1.0000
F81G	39	-1951.6325	4152.9397	0.0000	1.0000
JC69G	36	-1963.6120	4157.6930	0.0000	1.0000
F81IG	40	-1951.1439	4158.3645	0.0000	1.0000
F81I	39	-1955.1064	4159.8876	0.0000	1.0000
JC69IG	37	-1963.0544	4162.9796	0.0000	1.0000
JC69I	36	-1967.1181	4164.7052	0.0000	1.0000
F81	38	-1976.5042	4196.2813	0.0000	1.0000
JC69	35	-1989.4999	4203.0669	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11569.phylip = 1 - 603;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11569.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11569.phylip = 1 - 603;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11569.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;


[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/chrZ_11569.phylip = 1 - 603;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11569.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

