
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:37 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/chr12_5970.phylip" (19 taxa, 585 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	-2300.7840	4696.9013	0.7307	0.7307
GTRIG	45	-2300.6222	4698.9252	0.2656	0.9963
GTRI	44	-2306.1796	4707.6926	0.0033	0.9996
HKYG	40	-2313.1917	4712.4128	0.0003	0.9999
HKYIG	41	-2313.0240	4714.3905	0.0001	1.0000
HKYI	40	-2318.0232	4722.0758	0.0000	1.0000
SYMG	41	-2328.2673	4744.8771	0.0000	1.0000
K2PG	37	-2333.5555	4746.2518	0.0000	1.0000
SYMIG	42	-2328.0950	4746.8541	0.0000	1.0000
K2PIG	38	-2333.3771	4748.1828	0.0000	1.0000
SYMI	41	-2332.7157	4753.7739	0.0000	1.0000
K2PI	37	-2338.2330	4755.6069	0.0000	1.0000
GTR	43	-2336.4994	4765.9933	0.0000	1.0000
HKY	39	-2347.8672	4779.4592	0.0000	1.0000
SYM	40	-2362.0154	4810.0602	0.0000	1.0000
K2P	36	-2368.0696	4813.0005	0.0000	1.0000
F81G	39	-2381.3841	4846.4930	0.0000	1.0000
F81IG	40	-2381.2198	4848.4691	0.0000	1.0000
F81I	39	-2385.7061	4855.1370	0.0000	1.0000
JC69G	36	-2395.8768	4868.6150	0.0000	1.0000
JC69IG	37	-2395.7126	4870.5660	0.0000	1.0000
JC69I	36	-2400.1774	4877.2161	0.0000	1.0000
F81	38	-2413.6549	4908.7385	0.0000	1.0000
JC69	35	-2428.2641	4931.1184	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2300.7840	4689.5680	0.6957	0.6957
GTRIG	45	-2300.6222	4691.2443	0.3009	0.9966
GTRI	44	-2306.1796	4700.3593	0.0032	0.9998
HKYG	40	-2313.1917	4706.3833	0.0002	0.9999
HKYIG	41	-2313.0240	4708.0480	0.0001	1.0000
HKYI	40	-2318.0232	4716.0464	0.0000	1.0000
SYMG	41	-2328.2673	4738.5346	0.0000	1.0000
SYMIG	42	-2328.0950	4740.1899	0.0000	1.0000
K2PG	37	-2333.5555	4741.1110	0.0000	1.0000
K2PIG	38	-2333.3771	4742.7542	0.0000	1.0000
SYMI	41	-2332.7157	4747.4314	0.0000	1.0000
K2PI	37	-2338.2330	4750.4661	0.0000	1.0000
GTR	43	-2336.4994	4758.9989	0.0000	1.0000
HKY	39	-2347.8672	4773.7344	0.0000	1.0000
SYM	40	-2362.0154	4804.0307	0.0000	1.0000
K2P	36	-2368.0696	4808.1392	0.0000	1.0000
F81G	39	-2381.3841	4840.7682	0.0000	1.0000
F81IG	40	-2381.2198	4842.4397	0.0000	1.0000
F81I	39	-2385.7061	4849.4122	0.0000	1.0000
JC69G	36	-2395.8768	4863.7536	0.0000	1.0000
JC69IG	37	-2395.7126	4865.4253	0.0000	1.0000
JC69I	36	-2400.1774	4872.3548	0.0000	1.0000
F81	38	-2413.6549	4903.3099	0.0000	1.0000
JC69	35	-2428.2641	4926.5282	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2313.1917	4881.2478	0.5525	0.5525
GTRG	44	-2300.7840	4881.9189	0.3950	0.9476
HKYIG	41	-2313.0240	4887.2841	0.0270	0.9746
GTRIG	45	-2300.6222	4887.9669	0.0192	0.9938
HKYI	40	-2318.0232	4890.9108	0.0044	0.9982
GTRI	44	-2306.1796	4892.7102	0.0018	1.0000
K2PG	37	-2333.5555	4902.8607	0.0000	1.0000
K2PIG	38	-2333.3771	4908.8755	0.0000	1.0000
K2PI	37	-2338.2330	4912.2157	0.0000	1.0000
SYMG	41	-2328.2673	4917.7706	0.0000	1.0000
SYMIG	42	-2328.0950	4923.7976	0.0000	1.0000
SYMI	41	-2332.7157	4926.6674	0.0000	1.0000
HKY	39	-2347.8672	4944.2273	0.0000	1.0000
GTR	43	-2336.4994	4946.9782	0.0000	1.0000
K2P	36	-2368.0696	4965.5172	0.0000	1.0000
SYM	40	-2362.0154	4978.8952	0.0000	1.0000
F81G	39	-2381.3841	5011.2611	0.0000	1.0000
F81IG	40	-2381.2198	5017.3042	0.0000	1.0000
F81I	39	-2385.7061	5019.9051	0.0000	1.0000
JC69G	36	-2395.8768	5021.1317	0.0000	1.0000
JC69IG	37	-2395.7126	5027.1749	0.0000	1.0000
JC69I	36	-2400.1774	5029.7328	0.0000	1.0000
F81	38	-2413.6549	5069.4311	0.0000	1.0000
JC69	35	-2428.2641	5079.5347	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/chr12_5970.phylip = 1 - 585;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5970.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/chr12_5970.phylip = 1 - 585;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5970.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/chr12_5970.phylip = 1 - 585;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr12_5970.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

