
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:08 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_8629.phylip" (19 taxa, 557 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	-1870.5178	3827.3922	0.5015	0.5015
HKYI	40	-1871.4111	3829.1788	0.2053	0.7068
HKYIG	41	-1870.5177	3829.7227	0.1564	0.8632
GTRG	44	-1867.6353	3831.0049	0.0824	0.9456
GTRI	44	-1868.7006	3833.1356	0.0284	0.9740
GTRIG	45	-1867.6351	3833.3719	0.0252	0.9992
HKY	39	-1878.1169	3840.2686	0.0008	1.0000
GTR	43	-1882.5783	3858.5328	0.0000	1.0000
K2PG	37	-1891.6660	3862.7501	0.0000	1.0000
K2PI	37	-1892.4209	3864.2599	0.0000	1.0000
K2PIG	38	-1891.6679	3865.0578	0.0000	1.0000
SYMG	41	-1891.0961	3870.8796	0.0000	1.0000
SYMI	41	-1891.8844	3872.4561	0.0000	1.0000
SYMIG	42	-1891.0960	3873.2193	0.0000	1.0000
K2P	36	-1898.4900	3874.1031	0.0000	1.0000
F81G	39	-1897.2367	3878.5082	0.0000	1.0000
F81I	39	-1898.0996	3880.2341	0.0000	1.0000
F81IG	40	-1897.2366	3880.8298	0.0000	1.0000
SYM	40	-1897.9504	3882.2573	0.0000	1.0000
F81	38	-1910.2912	3902.3044	0.0000	1.0000
JC69G	36	-1917.8050	3912.7331	0.0000	1.0000
JC69I	36	-1918.5795	3914.2820	0.0000	1.0000
JC69IG	37	-1917.8049	3915.0279	0.0000	1.0000
JC69	35	-1930.1017	3935.0403	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1870.5178	3821.0356	0.4276	0.4276
HKYI	40	-1871.4111	3822.8222	0.1750	0.6026
HKYIG	41	-1870.5177	3823.0353	0.1573	0.7599
GTRG	44	-1867.6353	3823.2705	0.1399	0.8998
GTRIG	45	-1867.6351	3825.2702	0.0515	0.9512
GTRI	44	-1868.7006	3825.4012	0.0482	0.9994
HKY	39	-1878.1169	3834.2337	0.0006	1.0000
GTR	43	-1882.5783	3851.1566	0.0000	1.0000
K2PG	37	-1891.6660	3857.3319	0.0000	1.0000
K2PI	37	-1892.4209	3858.8418	0.0000	1.0000
K2PIG	38	-1891.6679	3859.3358	0.0000	1.0000
SYMG	41	-1891.0961	3864.1922	0.0000	1.0000
SYMI	41	-1891.8844	3865.7688	0.0000	1.0000
SYMIG	42	-1891.0960	3866.1920	0.0000	1.0000
K2P	36	-1898.4900	3868.9800	0.0000	1.0000
F81G	39	-1897.2367	3872.4734	0.0000	1.0000
F81I	39	-1898.0996	3874.1992	0.0000	1.0000
F81IG	40	-1897.2366	3874.4732	0.0000	1.0000
SYM	40	-1897.9504	3875.9008	0.0000	1.0000
F81	38	-1910.2912	3896.5824	0.0000	1.0000
JC69G	36	-1917.8050	3907.6100	0.0000	1.0000
JC69I	36	-1918.5795	3909.1589	0.0000	1.0000
JC69IG	37	-1917.8049	3909.6098	0.0000	1.0000
JC69	35	-1930.1017	3930.2034	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1870.5178	3993.9382	0.6832	0.6832
HKYI	40	-1871.4111	3995.7248	0.2797	0.9629
HKYIG	41	-1870.5177	4000.2605	0.0290	0.9919
HKY	39	-1878.1169	4002.8138	0.0081	0.9999
GTRG	44	-1867.6353	4013.4634	0.0000	1.0000
GTRI	44	-1868.7006	4015.5941	0.0000	1.0000
K2PG	37	-1891.6660	4017.2669	0.0000	1.0000
K2PI	37	-1892.4209	4018.7767	0.0000	1.0000
GTRIG	45	-1867.6351	4019.7856	0.0000	1.0000
K2PIG	38	-1891.6679	4023.5933	0.0000	1.0000
K2P	36	-1898.4900	4024.5923	0.0000	1.0000
GTR	43	-1882.5783	4037.0269	0.0000	1.0000
F81G	39	-1897.2367	4041.0535	0.0000	1.0000
SYMG	41	-1891.0961	4041.4174	0.0000	1.0000
F81I	39	-1898.0996	4042.7793	0.0000	1.0000
SYMI	41	-1891.8844	4042.9939	0.0000	1.0000
F81IG	40	-1897.2366	4047.3758	0.0000	1.0000
SYMIG	42	-1891.0960	4047.7398	0.0000	1.0000
SYM	40	-1897.9504	4048.8034	0.0000	1.0000
F81	38	-1910.2912	4060.8399	0.0000	1.0000
JC69G	36	-1917.8050	4063.2223	0.0000	1.0000
JC69I	36	-1918.5795	4064.7713	0.0000	1.0000
JC69IG	37	-1917.8049	4069.5447	0.0000	1.0000
JC69	35	-1930.1017	4081.4932	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/chr2_8629.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8629.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/chr2_8629.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8629.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/chr2_8629.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8629.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

