
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:51 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_17623.phylip" (19 taxa, 508 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	-1894.6190	3885.7908	0.8221	0.8221
HKYG	40	-1901.4053	3889.8341	0.1089	0.9310
HKYIG	41	-1901.2458	3891.8821	0.0391	0.9701
GTRIG	45	-1897.2758	3893.5127	0.0173	0.9874
GTRI	44	-1899.0444	3894.6417	0.0098	0.9972
HKYI	40	-1905.0713	3897.1661	0.0028	1.0000
K2PG	37	-1915.6863	3911.3556	0.0000	1.0000
K2PIG	38	-1915.5393	3913.3985	0.0000	1.0000
SYMG	41	-1912.7552	3914.9009	0.0000	1.0000
SYMIG	42	-1912.5922	3916.9522	0.0000	1.0000
K2PI	37	-1918.5793	3917.1416	0.0000	1.0000
SYMI	41	-1915.7948	3920.9802	0.0000	1.0000
GTR	43	-1923.0663	3940.2878	0.0000	1.0000
HKY	39	-1929.4155	3943.4978	0.0000	1.0000
K2P	36	-1944.1320	3965.9200	0.0000	1.0000
SYM	40	-1941.0139	3969.0514	0.0000	1.0000
F81IG	40	-1961.7399	4010.5034	0.0000	1.0000
F81G	39	-1964.2093	4013.0853	0.0000	1.0000
F81I	39	-1967.0665	4018.7997	0.0000	1.0000
JC69G	36	-1974.6010	4026.8580	0.0000	1.0000
JC69IG	37	-1974.5216	4029.0262	0.0000	1.0000
JC69I	36	-1977.2006	4032.0574	0.0000	1.0000
F81	38	-1990.2777	4062.8753	0.0000	1.0000
JC69	35	-2000.9658	4077.2706	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1894.6190	3877.2379	0.8868	0.8868
HKYG	40	-1901.4053	3882.8106	0.0547	0.9415
HKYIG	41	-1901.2458	3884.4916	0.0236	0.9651
GTRIG	45	-1897.2758	3884.5517	0.0229	0.9880
GTRI	44	-1899.0444	3886.0888	0.0106	0.9986
HKYI	40	-1905.0713	3890.1426	0.0014	1.0000
K2PG	37	-1915.6863	3905.3726	0.0000	1.0000
K2PIG	38	-1915.5393	3907.0787	0.0000	1.0000
SYMG	41	-1912.7552	3907.5103	0.0000	1.0000
SYMIG	42	-1912.5922	3909.1844	0.0000	1.0000
K2PI	37	-1918.5793	3911.1586	0.0000	1.0000
SYMI	41	-1915.7948	3913.5896	0.0000	1.0000
GTR	43	-1923.0663	3932.1326	0.0000	1.0000
HKY	39	-1929.4155	3936.8311	0.0000	1.0000
K2P	36	-1944.1320	3960.2640	0.0000	1.0000
SYM	40	-1941.0139	3962.0278	0.0000	1.0000
F81IG	40	-1961.7399	4003.4798	0.0000	1.0000
F81G	39	-1964.2093	4006.4186	0.0000	1.0000
F81I	39	-1967.0665	4012.1330	0.0000	1.0000
JC69G	36	-1974.6010	4021.2019	0.0000	1.0000
JC69IG	37	-1974.5216	4023.0432	0.0000	1.0000
JC69I	36	-1977.2006	4026.4013	0.0000	1.0000
F81	38	-1990.2777	4056.5554	0.0000	1.0000
JC69	35	-2000.9658	4071.9316	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1901.4053	4052.0298	0.9182	0.9182
HKYIG	41	-1901.2458	4057.9413	0.0478	0.9660
HKYI	40	-1905.0713	4059.3618	0.0235	0.9895
K2PG	37	-1915.6863	4061.9004	0.0066	0.9961
GTRG	44	-1894.6190	4063.3791	0.0032	0.9992
K2PI	37	-1918.5793	4067.6864	0.0004	0.9996
K2PIG	38	-1915.5393	4067.8370	0.0003	1.0000
GTRI	44	-1899.0444	4072.2300	0.0000	1.0000
GTRIG	45	-1897.2758	4074.9233	0.0000	1.0000
SYMG	41	-1912.7552	4080.9601	0.0000	1.0000
SYMIG	42	-1912.5922	4086.8647	0.0000	1.0000
SYMI	41	-1915.7948	4087.0394	0.0000	1.0000
HKY	39	-1929.4155	4101.8199	0.0000	1.0000
K2P	36	-1944.1320	4112.5613	0.0000	1.0000
GTR	43	-1923.0663	4114.0433	0.0000	1.0000
SYM	40	-1941.0139	4131.2471	0.0000	1.0000
F81G	39	-1964.2093	4171.4074	0.0000	1.0000
F81IG	40	-1961.7399	4172.6991	0.0000	1.0000
JC69G	36	-1974.6010	4173.4992	0.0000	1.0000
F81I	39	-1967.0665	4177.1218	0.0000	1.0000
JC69I	36	-1977.2006	4178.6986	0.0000	1.0000
JC69IG	37	-1974.5216	4179.5710	0.0000	1.0000
F81	38	-1990.2777	4217.3137	0.0000	1.0000
JC69	35	-2000.9658	4219.9985	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_17623.phylip = 1 - 508;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17623.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_17623.phylip = 1 - 508;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17623.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/chr3_17623.phylip = 1 - 508;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_17623.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;


-------------------------------------------------------------
End of Output

