
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:07 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/chr1_28726.phylip" (19 taxa, 594 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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	-2461.1606	5008.2524	0.3588	0.3588
K2PG	37	-2464.8025	5008.6625	0.2923	0.6511
HKYIG	41	-2461.1233	5010.4858	0.1175	0.7685
K2PIG	38	-2464.7650	5010.8706	0.0969	0.8654
GTRG	44	-2458.4063	5012.0258	0.0544	0.9198
HKYI	40	-2463.7503	5013.4318	0.0269	0.9467
K2PI	37	-2467.2771	5013.6118	0.0246	0.9714
GTRIG	45	-2458.3543	5014.2633	0.0178	0.9891
SYMG	41	-2464.0677	5016.3745	0.0062	0.9953
GTRI	44	-2461.6134	5018.4400	0.0022	0.9975
SYMIG	42	-2464.0247	5018.6047	0.0020	0.9995
SYMI	41	-2466.6437	5021.5266	0.0005	1.0000
HKY	39	-2501.4400	5086.5117	0.0000	1.0000
K2P	36	-2504.8912	5086.5652	0.0000	1.0000
GTR	43	-2498.1056	5089.0913	0.0000	1.0000
SYM	40	-2503.7372	5093.4057	0.0000	1.0000
JC69G	36	-2523.5041	5123.7910	0.0000	1.0000
F81G	39	-2520.4717	5124.5752	0.0000	1.0000
JC69IG	37	-2523.4712	5126.0000	0.0000	1.0000
F81IG	40	-2520.4327	5126.7968	0.0000	1.0000
JC69I	36	-2525.7495	5128.2817	0.0000	1.0000
F81I	39	-2522.8292	5129.2901	0.0000	1.0000
JC69	35	-2562.0585	5198.6332	0.0000	1.0000
F81	38	-2558.7565	5198.8536	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2461.1606	5002.3212	0.3747	0.3747
K2PG	37	-2464.8025	5003.6050	0.1972	0.5719
HKYIG	41	-2461.1233	5004.2467	0.1431	0.7150
GTRG	44	-2458.4063	5004.8127	0.1078	0.8228
K2PIG	38	-2464.7650	5005.5301	0.0753	0.8981
GTRIG	45	-2458.3543	5006.7085	0.0418	0.9399
HKYI	40	-2463.7503	5007.5005	0.0281	0.9680
K2PI	37	-2467.2771	5008.5542	0.0166	0.9846
SYMG	41	-2464.0677	5010.1354	0.0075	0.9922
GTRI	44	-2461.6134	5011.2268	0.0044	0.9965
SYMIG	42	-2464.0247	5012.0493	0.0029	0.9994
SYMI	41	-2466.6437	5015.2874	0.0006	1.0000
HKY	39	-2501.4400	5080.8800	0.0000	1.0000
K2P	36	-2504.8912	5081.7825	0.0000	1.0000
GTR	43	-2498.1056	5082.2113	0.0000	1.0000
SYM	40	-2503.7372	5087.4744	0.0000	1.0000
F81G	39	-2520.4717	5118.9434	0.0000	1.0000
JC69G	36	-2523.5041	5119.0083	0.0000	1.0000
F81IG	40	-2520.4327	5120.8655	0.0000	1.0000
JC69IG	37	-2523.4712	5120.9424	0.0000	1.0000
JC69I	36	-2525.7495	5123.4990	0.0000	1.0000
F81I	39	-2522.8292	5123.6583	0.0000	1.0000
F81	38	-2558.7565	5193.5131	0.0000	1.0000
JC69	35	-2562.0585	5194.1171	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2464.8025	5165.9195	0.8852	0.8852
K2PI	37	-2467.2771	5170.8688	0.0745	0.9597
K2PIG	38	-2464.7650	5172.2315	0.0377	0.9974
HKYG	40	-2461.1606	5177.7963	0.0023	0.9997
HKYI	40	-2463.7503	5182.9757	0.0002	0.9999
HKYIG	41	-2461.1233	5184.1088	0.0001	1.0000
SYMG	41	-2464.0677	5189.9975	0.0000	1.0000
SYMI	41	-2466.6437	5195.1495	0.0000	1.0000
SYMIG	42	-2464.0247	5196.2983	0.0000	1.0000
GTRG	44	-2458.4063	5197.8354	0.0000	1.0000
GTRIG	45	-2458.3543	5204.1181	0.0000	1.0000
GTRI	44	-2461.6134	5204.2495	0.0000	1.0000
K2P	36	-2504.8912	5239.7101	0.0000	1.0000
HKY	39	-2501.4400	5251.9683	0.0000	1.0000
SYM	40	-2503.7372	5262.9496	0.0000	1.0000
GTR	43	-2498.1056	5270.8471	0.0000	1.0000
JC69G	36	-2523.5041	5276.9359	0.0000	1.0000
JC69I	36	-2525.7495	5281.4266	0.0000	1.0000
JC69IG	37	-2523.4712	5283.2570	0.0000	1.0000
F81G	39	-2520.4717	5290.0317	0.0000	1.0000
F81I	39	-2522.8292	5294.7466	0.0000	1.0000
F81IG	40	-2520.4327	5296.3407	0.0000	1.0000
JC69	35	-2562.0585	5347.6579	0.0000	1.0000
F81	38	-2558.7565	5360.2145	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/chr1_28726.phylip = 1 - 594;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28726.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/chr1_28726.phylip = 1 - 594;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28726.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28726.phylip = 1 - 594;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28726.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

