
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:04 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/chr11_3445.phylip" (19 taxa, 836 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	-2852.5709	5798.1482	0.3833	0.3833
GTRIG	45	-2851.6768	5798.5942	0.3067	0.6900
HKYG	40	-2857.8040	5799.7339	0.1735	0.8635
HKYIG	41	-2857.0069	5800.3514	0.1274	0.9908
GTRI	44	-2856.8131	5806.6324	0.0055	0.9963
HKYI	40	-2861.6646	5807.4550	0.0037	1.0000
K2PG	37	-2882.9807	5843.4852	0.0000	1.0000
SYMG	41	-2878.7379	5843.8134	0.0000	1.0000
K2PIG	38	-2882.1582	5844.0353	0.0000	1.0000
SYMIG	42	-2877.9131	5844.3812	0.0000	1.0000
K2PI	37	-2886.8698	5851.2635	0.0000	1.0000
SYMI	41	-2882.5770	5851.4916	0.0000	1.0000
HKY	39	-2909.9219	5901.7633	0.0000	1.0000
GTR	43	-2905.5133	5901.8044	0.0000	1.0000
SYM	40	-2929.7637	5943.6531	0.0000	1.0000
K2P	36	-2934.7254	5944.7849	0.0000	1.0000
F81G	39	-2943.4296	5968.7789	0.0000	1.0000
F81IG	40	-2943.0177	5970.1613	0.0000	1.0000
F81I	39	-2946.1067	5974.1330	0.0000	1.0000
JC69G	36	-2967.1761	6009.6863	0.0000	1.0000
JC69IG	37	-2966.7645	6011.0528	0.0000	1.0000
JC69I	36	-2969.7127	6014.7595	0.0000	1.0000
F81	38	-2991.1614	6062.0417	0.0000	1.0000
JC69	35	-3013.7731	6100.6963	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2852.5709	5793.1419	0.4083	0.4083
GTRIG	45	-2851.6768	5793.3537	0.3673	0.7755
HKYG	40	-2857.8040	5795.6081	0.1190	0.8945
HKYIG	41	-2857.0069	5796.0139	0.0971	0.9916
GTRI	44	-2856.8131	5801.6261	0.0059	0.9975
HKYI	40	-2861.6646	5803.3292	0.0025	1.0000
SYMG	41	-2878.7379	5839.4759	0.0000	1.0000
SYMIG	42	-2877.9131	5839.8263	0.0000	1.0000
K2PG	37	-2882.9807	5839.9614	0.0000	1.0000
K2PIG	38	-2882.1582	5840.3163	0.0000	1.0000
SYMI	41	-2882.5770	5847.1541	0.0000	1.0000
K2PI	37	-2886.8698	5847.7397	0.0000	1.0000
GTR	43	-2905.5133	5897.0266	0.0000	1.0000
HKY	39	-2909.9219	5897.8437	0.0000	1.0000
SYM	40	-2929.7637	5939.5274	0.0000	1.0000
K2P	36	-2934.7254	5941.4508	0.0000	1.0000
F81G	39	-2943.4296	5964.8593	0.0000	1.0000
F81IG	40	-2943.0177	5966.0355	0.0000	1.0000
F81I	39	-2946.1067	5970.2134	0.0000	1.0000
JC69G	36	-2967.1761	6006.3521	0.0000	1.0000
JC69IG	37	-2966.7645	6007.5290	0.0000	1.0000
JC69I	36	-2969.7127	6011.4253	0.0000	1.0000
F81	38	-2991.1614	6058.3228	0.0000	1.0000
JC69	35	-3013.7731	6097.5463	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2857.8040	5984.7532	0.9107	0.9107
HKYIG	41	-2857.0069	5989.8877	0.0699	0.9806
HKYI	40	-2861.6646	5992.4743	0.0192	0.9997
GTRG	44	-2852.5709	6001.2015	0.0002	1.0000
GTRIG	45	-2851.6768	6006.1419	0.0000	1.0000
GTRI	44	-2856.8131	6009.6858	0.0000	1.0000
K2PG	37	-2882.9807	6014.9207	0.0000	1.0000
K2PIG	38	-2882.1582	6020.0042	0.0000	1.0000
K2PI	37	-2886.8698	6022.6989	0.0000	1.0000
SYMG	41	-2878.7379	6033.3496	0.0000	1.0000
SYMIG	42	-2877.9131	6038.4287	0.0000	1.0000
SYMI	41	-2882.5770	6041.0279	0.0000	1.0000
HKY	39	-2909.9219	6082.2603	0.0000	1.0000
GTR	43	-2905.5133	6100.3576	0.0000	1.0000
K2P	36	-2934.7254	6111.6814	0.0000	1.0000
SYM	40	-2929.7637	6128.6725	0.0000	1.0000
F81G	39	-2943.4296	6149.2758	0.0000	1.0000
F81I	39	-2946.1067	6154.6299	0.0000	1.0000
F81IG	40	-2943.0177	6155.1806	0.0000	1.0000
JC69G	36	-2967.1761	6176.5828	0.0000	1.0000
JC69I	36	-2969.7127	6181.6560	0.0000	1.0000
JC69IG	37	-2966.7645	6182.4882	0.0000	1.0000
F81	38	-2991.1614	6238.0106	0.0000	1.0000
JC69	35	-3013.7731	6263.0483	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/chr11_3445.phylip = 1 - 836;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3445.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/chr11_3445.phylip = 1 - 836;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3445.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/chr11_3445.phylip = 1 - 836;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3445.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

