
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:15 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_11267.phylip" (19 taxa, 540 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	-2301.6395	4699.2789	0.7638	0.7638
GTRIG	45	-2301.6276	4701.6358	0.2351	0.9988
HKYG	40	-2313.1550	4712.8832	0.0008	0.9997
HKYIG	41	-2313.1396	4715.1949	0.0003	0.9999
GTRI	44	-2310.8380	4717.6760	0.0001	1.0000
HKYI	40	-2320.6854	4727.9439	0.0000	1.0000
K2PG	37	-2328.8434	4737.2883	0.0000	1.0000
SYMG	41	-2324.8480	4738.6116	0.0000	1.0000
K2PIG	38	-2328.8143	4739.5447	0.0000	1.0000
SYMIG	42	-2324.8226	4740.9128	0.0000	1.0000
K2PI	37	-2335.8437	4751.2891	0.0000	1.0000
SYMI	41	-2332.0149	4752.9455	0.0000	1.0000
GTR	43	-2340.8297	4775.2885	0.0000	1.0000
HKY	39	-2349.6328	4783.5055	0.0000	1.0000
K2P	36	-2365.4755	4808.2472	0.0000	1.0000
SYM	40	-2361.4834	4809.5399	0.0000	1.0000
F81G	39	-2366.3273	4816.8945	0.0000	1.0000
F81IG	40	-2366.3271	4819.2273	0.0000	1.0000
F81I	39	-2372.7804	4829.8008	0.0000	1.0000
JC69G	36	-2377.3488	4831.9938	0.0000	1.0000
JC69IG	37	-2377.3427	4834.2870	0.0000	1.0000
JC69I	36	-2383.6195	4844.5352	0.0000	1.0000
F81	38	-2400.3483	4882.6128	0.0000	1.0000
JC69	35	-2411.6550	4898.3101	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2301.6395	4691.2789	0.7283	0.7283
GTRIG	45	-2301.6276	4693.2552	0.2711	0.9994
HKYG	40	-2313.1550	4706.3101	0.0004	0.9998
HKYIG	41	-2313.1396	4708.2792	0.0001	0.9999
GTRI	44	-2310.8380	4709.6760	0.0001	1.0000
HKYI	40	-2320.6854	4721.3708	0.0000	1.0000
K2PG	37	-2328.8434	4731.6867	0.0000	1.0000
SYMG	41	-2324.8480	4731.6959	0.0000	1.0000
K2PIG	38	-2328.8143	4733.6285	0.0000	1.0000
SYMIG	42	-2324.8226	4733.6452	0.0000	1.0000
K2PI	37	-2335.8437	4745.6875	0.0000	1.0000
SYMI	41	-2332.0149	4746.0299	0.0000	1.0000
GTR	43	-2340.8297	4767.6595	0.0000	1.0000
HKY	39	-2349.6328	4777.2655	0.0000	1.0000
K2P	36	-2365.4755	4802.9510	0.0000	1.0000
SYM	40	-2361.4834	4802.9667	0.0000	1.0000
F81G	39	-2366.3273	4810.6545	0.0000	1.0000
F81IG	40	-2366.3271	4812.6542	0.0000	1.0000
F81I	39	-2372.7804	4823.5608	0.0000	1.0000
JC69G	36	-2377.3488	4826.6976	0.0000	1.0000
JC69IG	37	-2377.3427	4828.6854	0.0000	1.0000
JC69I	36	-2383.6195	4839.2390	0.0000	1.0000
F81	38	-2400.3483	4876.6967	0.0000	1.0000
JC69	35	-2411.6550	4893.3101	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2313.1550	4877.9728	0.7117	0.7117
GTRG	44	-2301.6395	4880.1079	0.2447	0.9564
HKYIG	41	-2313.1396	4884.2335	0.0311	0.9875
GTRIG	45	-2301.6276	4886.3758	0.0107	0.9982
K2PG	37	-2328.8434	4890.4748	0.0014	0.9995
HKYI	40	-2320.6854	4893.0335	0.0004	0.9999
K2PIG	38	-2328.8143	4896.7081	0.0001	1.0000
GTRI	44	-2310.8380	4898.5050	0.0000	1.0000
K2PI	37	-2335.8437	4904.4755	0.0000	1.0000
SYMG	41	-2324.8480	4907.6503	0.0000	1.0000
SYMIG	42	-2324.8226	4913.8911	0.0000	1.0000
SYMI	41	-2332.0149	4921.9842	0.0000	1.0000
HKY	39	-2349.6328	4944.6367	0.0000	1.0000
GTR	43	-2340.8297	4952.1970	0.0000	1.0000
K2P	36	-2365.4755	4957.4475	0.0000	1.0000
SYM	40	-2361.4834	4974.6295	0.0000	1.0000
F81G	39	-2366.3273	4978.0257	0.0000	1.0000
JC69G	36	-2377.3488	4981.1941	0.0000	1.0000
F81IG	40	-2366.3271	4984.3169	0.0000	1.0000
JC69IG	37	-2377.3427	4987.4735	0.0000	1.0000
F81I	39	-2372.7804	4990.9320	0.0000	1.0000
JC69I	36	-2383.6195	4993.7355	0.0000	1.0000
F81	38	-2400.3483	5039.7763	0.0000	1.0000
JC69	35	-2411.6550	5043.5150	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/chrZ_11267.phylip = 1 - 540;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11267.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/chrZ_11267.phylip = 1 - 540;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11267.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/chrZ_11267.phylip = 1 - 540;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_11267.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

