
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:22 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/chr1_5460.phylip" (19 taxa, 769 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	-3273.8890	6641.2477	0.6139	0.6139
GTRIG	45	-3273.2296	6642.1853	0.3842	0.9981
HKYG	40	-3285.0572	6654.6198	0.0008	0.9989
HKYIG	41	-3284.1851	6655.1075	0.0006	0.9995
GTRI	44	-3280.9151	6655.2999	0.0005	1.0000
HKYI	40	-3290.3567	6665.2188	0.0000	1.0000
K2PG	37	-3317.6570	6713.1607	0.0000	1.0000
K2PIG	38	-3316.7885	6713.6373	0.0000	1.0000
SYMG	41	-3315.8780	6718.4933	0.0000	1.0000
SYMIG	42	-3315.0657	6719.1066	0.0000	1.0000
K2PI	37	-3322.9556	6723.7580	0.0000	1.0000
SYMI	41	-3320.9414	6728.6201	0.0000	1.0000
F81G	39	-3352.4343	6787.1485	0.0000	1.0000
F81IG	40	-3351.7415	6787.9885	0.0000	1.0000
F81I	39	-3356.3892	6795.0582	0.0000	1.0000
JC69G	36	-3377.7311	6831.1015	0.0000	1.0000
JC69IG	37	-3377.0161	6831.8789	0.0000	1.0000
GTR	43	-3371.7821	6834.7835	0.0000	1.0000
JC69I	36	-3381.8366	6839.3125	0.0000	1.0000
HKY	39	-3385.0521	6852.3840	0.0000	1.0000
K2P	36	-3421.3169	6918.2731	0.0000	1.0000
SYM	40	-3417.5627	6919.6309	0.0000	1.0000
F81	38	-3446.5418	6973.1439	0.0000	1.0000
JC69	35	-3474.0435	7021.5249	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3273.8890	6635.7781	0.5835	0.5835
GTRIG	45	-3273.2296	6636.4591	0.4151	0.9986
GTRI	44	-3280.9151	6649.8303	0.0005	0.9992
HKYG	40	-3285.0572	6650.1143	0.0004	0.9996
HKYIG	41	-3284.1851	6650.3703	0.0004	1.0000
HKYI	40	-3290.3567	6660.7133	0.0000	1.0000
K2PG	37	-3317.6570	6709.3140	0.0000	1.0000
K2PIG	38	-3316.7885	6709.5770	0.0000	1.0000
SYMG	41	-3315.8780	6713.7560	0.0000	1.0000
SYMIG	42	-3315.0657	6714.1314	0.0000	1.0000
K2PI	37	-3322.9556	6719.9112	0.0000	1.0000
SYMI	41	-3320.9414	6723.8828	0.0000	1.0000
F81G	39	-3352.4343	6782.8687	0.0000	1.0000
F81IG	40	-3351.7415	6783.4830	0.0000	1.0000
F81I	39	-3356.3892	6790.7784	0.0000	1.0000
JC69G	36	-3377.7311	6827.4622	0.0000	1.0000
JC69IG	37	-3377.0161	6828.0321	0.0000	1.0000
GTR	43	-3371.7821	6829.5642	0.0000	1.0000
JC69I	36	-3381.8366	6835.6731	0.0000	1.0000
HKY	39	-3385.0521	6848.1041	0.0000	1.0000
K2P	36	-3421.3169	6914.6338	0.0000	1.0000
SYM	40	-3417.5627	6915.1254	0.0000	1.0000
F81	38	-3446.5418	6969.0836	0.0000	1.0000
JC69	35	-3474.0435	7018.0870	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3285.0572	6835.9179	0.8200	0.8200
GTRG	44	-3273.8890	6840.1621	0.0982	0.9182
HKYIG	41	-3284.1851	6840.8190	0.0707	0.9890
GTRIG	45	-3273.2296	6845.4882	0.0068	0.9958
HKYI	40	-3290.3567	6846.5170	0.0041	0.9999
GTRI	44	-3280.9151	6854.2143	0.0001	1.0000
K2PG	37	-3317.6570	6881.1823	0.0000	1.0000
K2PIG	38	-3316.7885	6886.0905	0.0000	1.0000
K2PI	37	-3322.9556	6891.7796	0.0000	1.0000
SYMG	41	-3315.8780	6904.2047	0.0000	1.0000
SYMIG	42	-3315.0657	6909.2252	0.0000	1.0000
SYMI	41	-3320.9414	6914.3315	0.0000	1.0000
F81G	39	-3352.4343	6964.0272	0.0000	1.0000
F81IG	40	-3351.7415	6969.2866	0.0000	1.0000
F81I	39	-3356.3892	6971.9369	0.0000	1.0000
JC69G	36	-3377.7311	6994.6855	0.0000	1.0000
JC69IG	37	-3377.0161	6999.9005	0.0000	1.0000
JC69I	36	-3381.8366	7002.8964	0.0000	1.0000
HKY	39	-3385.0521	7029.2627	0.0000	1.0000
GTR	43	-3371.7821	7029.3031	0.0000	1.0000
K2P	36	-3421.3169	7081.8570	0.0000	1.0000
SYM	40	-3417.5627	7100.9290	0.0000	1.0000
F81	38	-3446.5418	7145.5970	0.0000	1.0000
JC69	35	-3474.0435	7180.6651	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/chr1_5460.phylip = 1 - 769;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5460.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/chr1_5460.phylip = 1 - 769;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5460.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/chr1_5460.phylip = 1 - 769;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5460.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

