
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:42 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_3419.phylip" (19 taxa, 603 characters)

Minimum AIC  model: GTRG
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	-2875.3172	5836.4706	0.3561	0.3561
GTRG	44	-2870.8804	5836.8576	0.2935	0.6496
HKYIG	41	-2874.8519	5837.8428	0.1793	0.8289
GTRIG	45	-2870.3797	5838.1921	0.1506	0.9795
K2PG	37	-2882.2321	5843.4413	0.0109	0.9904
K2PIG	38	-2882.0319	5845.3192	0.0043	0.9946
SYMG	41	-2878.9959	5846.1308	0.0028	0.9975
SYMIG	42	-2878.6631	5847.7762	0.0012	0.9987
HKYI	40	-2881.4231	5848.6825	0.0008	0.9995
GTRI	44	-2877.3673	5849.8315	0.0004	1.0000
K2PI	37	-2888.4006	5855.7781	0.0000	1.0000
SYMI	41	-2885.0995	5858.3380	0.0000	1.0000
F81G	39	-2931.2645	5946.0708	0.0000	1.0000
F81IG	40	-2931.0062	5947.8486	0.0000	1.0000
JC69G	36	-2938.7238	5954.1543	0.0000	1.0000
JC69IG	37	-2938.4928	5955.9627	0.0000	1.0000
F81I	39	-2937.2725	5958.0867	0.0000	1.0000
JC69I	36	-2944.7196	5966.1459	0.0000	1.0000
GTR	43	-2955.4542	6003.6777	0.0000	1.0000
HKY	39	-2960.3838	6004.3093	0.0000	1.0000
K2P	36	-2969.0306	6014.7680	0.0000	1.0000
SYM	40	-2965.5506	6016.9375	0.0000	1.0000
F81	38	-3014.7577	6110.7708	0.0000	1.0000
JC69	35	-3023.3118	6121.0681	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2870.8804	5829.7608	0.3756	0.3756
HKYG	40	-2875.3172	5830.6343	0.2427	0.6183
GTRIG	45	-2870.3797	5830.7594	0.2280	0.8463
HKYIG	41	-2874.8519	5831.7037	0.1422	0.9884
K2PG	37	-2882.2321	5838.4643	0.0048	0.9933
SYMG	41	-2878.9959	5839.9918	0.0023	0.9955
K2PIG	38	-2882.0319	5840.0639	0.0022	0.9977
SYMIG	42	-2878.6631	5841.3262	0.0012	0.9989
GTRI	44	-2877.3673	5842.7347	0.0006	0.9994
HKYI	40	-2881.4231	5842.8462	0.0005	1.0000
K2PI	37	-2888.4006	5850.8011	0.0000	1.0000
SYMI	41	-2885.0995	5852.1990	0.0000	1.0000
F81G	39	-2931.2645	5940.5291	0.0000	1.0000
F81IG	40	-2931.0062	5942.0123	0.0000	1.0000
JC69G	36	-2938.7238	5949.4475	0.0000	1.0000
JC69IG	37	-2938.4928	5950.9857	0.0000	1.0000
F81I	39	-2937.2725	5952.5450	0.0000	1.0000
JC69I	36	-2944.7196	5961.4392	0.0000	1.0000
GTR	43	-2955.4542	5996.9085	0.0000	1.0000
HKY	39	-2960.3838	5998.7676	0.0000	1.0000
K2P	36	-2969.0306	6010.0613	0.0000	1.0000
SYM	40	-2965.5506	6011.1012	0.0000	1.0000
F81	38	-3014.7577	6105.5155	0.0000	1.0000
JC69	35	-3023.3118	6116.6237	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2882.2321	6001.3352	0.8893	0.8893
HKYG	40	-2875.3172	6006.7110	0.0605	0.9498
K2PIG	38	-2882.0319	6007.3367	0.0442	0.9940
HKYIG	41	-2874.8519	6012.1823	0.0039	0.9979
K2PI	37	-2888.4006	6013.6721	0.0019	0.9998
HKYI	40	-2881.4231	6018.9229	0.0001	0.9999
SYMG	41	-2878.9959	6020.4704	0.0001	1.0000
GTRG	44	-2870.8804	6023.4452	0.0000	1.0000
SYMIG	42	-2878.6631	6026.2067	0.0000	1.0000
GTRIG	45	-2870.3797	6028.8457	0.0000	1.0000
SYMI	41	-2885.0995	6032.6776	0.0000	1.0000
GTRI	44	-2877.3673	6036.4190	0.0000	1.0000
JC69G	36	-2938.7238	6107.9166	0.0000	1.0000
F81G	39	-2931.2645	6112.2039	0.0000	1.0000
JC69IG	37	-2938.4928	6113.8566	0.0000	1.0000
F81IG	40	-2931.0062	6118.0890	0.0000	1.0000
JC69I	36	-2944.7196	6119.9082	0.0000	1.0000
F81I	39	-2937.2725	6124.2197	0.0000	1.0000
K2P	36	-2969.0306	6168.5303	0.0000	1.0000
HKY	39	-2960.3838	6170.4424	0.0000	1.0000
GTR	43	-2955.4542	6186.1909	0.0000	1.0000
SYM	40	-2965.5506	6187.1779	0.0000	1.0000
JC69	35	-3023.3118	6270.6908	0.0000	1.0000
F81	38	-3014.7577	6272.7883	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_3419.phylip = 1 - 603;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3419.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3419.phylip = 1 - 603;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3419.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/chr11_3419.phylip = 1 - 603;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3419.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

