
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:25 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/chr3_7228.phylip" (19 taxa, 572 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	-2869.6150	5834.7443	0.6315	0.6315
GTRIG	45	-2869.0954	5836.0616	0.3268	0.9583
GTRI	44	-2872.3572	5840.2286	0.0407	0.9990
HKYG	40	-2881.1694	5848.5158	0.0006	0.9997
HKYIG	41	-2880.8445	5850.1872	0.0003	0.9999
HKYI	40	-2883.7083	5853.5937	0.0001	1.0000
GTR	43	-2905.8454	5904.8575	0.0000	1.0000
K2PG	37	-2918.2231	5915.7121	0.0000	1.0000
HKY	39	-2916.5065	5916.8776	0.0000	1.0000
K2PIG	38	-2918.1245	5917.8099	0.0000	1.0000
SYMG	41	-2916.2972	5921.0925	0.0000	1.0000
SYMIG	42	-2916.2099	5923.2479	0.0000	1.0000
K2PI	37	-2922.0902	5923.4464	0.0000	1.0000
SYMI	41	-2920.0750	5928.6482	0.0000	1.0000
K2P	36	-2956.6514	5990.2822	0.0000	1.0000
SYM	40	-2953.8801	5993.9371	0.0000	1.0000
F81G	39	-2973.8516	6031.5679	0.0000	1.0000
F81IG	40	-2973.6645	6033.5061	0.0000	1.0000
F81I	39	-2976.1524	6036.1695	0.0000	1.0000
JC69G	36	-2998.0388	6073.0570	0.0000	1.0000
JC69IG	37	-2997.9503	6075.1665	0.0000	1.0000
JC69I	36	-3001.1746	6079.3286	0.0000	1.0000
F81	38	-3007.0046	6095.5701	0.0000	1.0000
JC69	35	-3033.0076	6140.7167	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2869.6150	5827.2300	0.5939	0.5939
GTRIG	45	-2869.0954	5828.1909	0.3673	0.9612
GTRI	44	-2872.3572	5832.7143	0.0383	0.9995
HKYG	40	-2881.1694	5842.3388	0.0003	0.9998
HKYIG	41	-2880.8445	5843.6891	0.0002	1.0000
HKYI	40	-2883.7083	5847.4167	0.0000	1.0000
GTR	43	-2905.8454	5897.6908	0.0000	1.0000
K2PG	37	-2918.2231	5910.4461	0.0000	1.0000
HKY	39	-2916.5065	5911.0130	0.0000	1.0000
K2PIG	38	-2918.1245	5912.2489	0.0000	1.0000
SYMG	41	-2916.2972	5914.5944	0.0000	1.0000
SYMIG	42	-2916.2099	5916.4199	0.0000	1.0000
K2PI	37	-2922.0902	5918.1804	0.0000	1.0000
SYMI	41	-2920.0750	5922.1501	0.0000	1.0000
K2P	36	-2956.6514	5985.3028	0.0000	1.0000
SYM	40	-2953.8801	5987.7601	0.0000	1.0000
F81G	39	-2973.8516	6025.7033	0.0000	1.0000
F81IG	40	-2973.6645	6027.3291	0.0000	1.0000
F81I	39	-2976.1524	6030.3049	0.0000	1.0000
JC69G	36	-2998.0388	6068.0775	0.0000	1.0000
JC69IG	37	-2997.9503	6069.9006	0.0000	1.0000
JC69I	36	-3001.1746	6074.3492	0.0000	1.0000
F81	38	-3007.0046	6090.0091	0.0000	1.0000
JC69	35	-3033.0076	6136.0152	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2881.1694	6016.3043	0.6674	0.6674
GTRG	44	-2869.6150	6018.5922	0.2126	0.8800
HKYI	40	-2883.7083	6021.3822	0.0527	0.9327
HKYIG	41	-2880.8445	6022.0038	0.0386	0.9714
GTRIG	45	-2869.0954	6023.9021	0.0149	0.9863
GTRI	44	-2872.3572	6024.0764	0.0137	1.0000
K2PG	37	-2918.2231	6071.3643	0.0000	1.0000
K2PIG	38	-2918.1245	6077.5162	0.0000	1.0000
K2PI	37	-2922.0902	6079.0986	0.0000	1.0000
HKY	39	-2916.5065	6080.6294	0.0000	1.0000
GTR	43	-2905.8454	6084.7038	0.0000	1.0000
SYMG	41	-2916.2972	6092.9091	0.0000	1.0000
SYMIG	42	-2916.2099	6099.0837	0.0000	1.0000
SYMI	41	-2920.0750	6100.4648	0.0000	1.0000
K2P	36	-2956.6514	6141.8718	0.0000	1.0000
SYM	40	-2953.8801	6161.7257	0.0000	1.0000
F81G	39	-2973.8516	6195.3197	0.0000	1.0000
F81I	39	-2976.1524	6199.9213	0.0000	1.0000
F81IG	40	-2973.6645	6201.2946	0.0000	1.0000
JC69G	36	-2998.0388	6224.6465	0.0000	1.0000
JC69IG	37	-2997.9503	6230.8187	0.0000	1.0000
JC69I	36	-3001.1746	6230.9182	0.0000	1.0000
F81	38	-3007.0046	6255.2764	0.0000	1.0000
JC69	35	-3033.0076	6288.2350	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/chr3_7228.phylip = 1 - 572;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7228.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/chr3_7228.phylip = 1 - 572;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7228.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/chr3_7228.phylip = 1 - 572;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7228.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

