
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:05 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/chr8_3325.phylip" (19 taxa, 359 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	-1384.0031	2858.3207	0.6359	0.6359
HKYIG	41	-1383.9654	2860.7952	0.1845	0.8204
GTRG	44	-1380.8742	2862.3599	0.0844	0.9048
HKYI	40	-1386.5526	2863.4196	0.0497	0.9545
GTRIG	45	-1380.8031	2864.8331	0.0245	0.9790
GTRI	44	-1382.6530	2865.9176	0.0142	0.9932
K2PG	37	-1392.6500	2868.0602	0.0049	0.9981
K2PIG	38	-1392.6017	2870.4659	0.0015	0.9996
K2PI	37	-1395.3984	2873.5570	0.0003	0.9999
SYMG	41	-1391.7594	2876.3832	0.0001	1.0000
SYMIG	42	-1391.7136	2878.8575	0.0000	1.0000
SYMI	41	-1394.4292	2881.7228	0.0000	1.0000
HKY	39	-1406.5241	2900.8287	0.0000	1.0000
GTR	43	-1402.8227	2903.6581	0.0000	1.0000
K2P	36	-1415.2148	2910.7029	0.0000	1.0000
SYM	40	-1414.3140	2918.9424	0.0000	1.0000
F81G	39	-1428.6986	2945.1777	0.0000	1.0000
F81IG	40	-1428.6670	2947.6484	0.0000	1.0000
F81I	39	-1431.0472	2949.8750	0.0000	1.0000
JC69G	36	-1436.4516	2953.1765	0.0000	1.0000
JC69IG	37	-1436.4223	2955.6048	0.0000	1.0000
JC69I	36	-1439.0693	2958.4118	0.0000	1.0000
F81	38	-1449.5492	2984.3610	0.0000	1.0000
JC69	35	-1457.5071	2992.8161	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1384.0031	2848.0062	0.4717	0.4717
GTRG	44	-1380.8742	2849.7484	0.1974	0.6691
HKYIG	41	-1383.9654	2849.9309	0.1802	0.8493
GTRIG	45	-1380.8031	2851.6063	0.0780	0.9273
HKYI	40	-1386.5526	2853.1051	0.0369	0.9641
GTRI	44	-1382.6530	2853.3061	0.0333	0.9975
K2PG	37	-1392.6500	2859.3001	0.0017	0.9991
K2PIG	38	-1392.6017	2861.2034	0.0006	0.9998
K2PI	37	-1395.3984	2864.7969	0.0001	0.9999
SYMG	41	-1391.7594	2865.5188	0.0001	1.0000
SYMIG	42	-1391.7136	2867.4271	0.0000	1.0000
SYMI	41	-1394.4292	2870.8584	0.0000	1.0000
HKY	39	-1406.5241	2891.0481	0.0000	1.0000
GTR	43	-1402.8227	2891.6454	0.0000	1.0000
K2P	36	-1415.2148	2902.4296	0.0000	1.0000
SYM	40	-1414.3140	2908.6280	0.0000	1.0000
F81G	39	-1428.6986	2935.3971	0.0000	1.0000
F81IG	40	-1428.6670	2937.3340	0.0000	1.0000
F81I	39	-1431.0472	2940.0944	0.0000	1.0000
JC69G	36	-1436.4516	2944.9032	0.0000	1.0000
JC69IG	37	-1436.4223	2946.8447	0.0000	1.0000
JC69I	36	-1439.0693	2950.1385	0.0000	1.0000
F81	38	-1449.5492	2975.0985	0.0000	1.0000
JC69	35	-1457.5071	2985.0142	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1392.6500	3002.9830	0.4836	0.4836
HKYG	40	-1384.0031	3003.3391	0.4047	0.8883
HKYI	40	-1386.5526	3008.4380	0.0316	0.9200
K2PI	37	-1395.3984	3008.4798	0.0310	0.9509
K2PIG	38	-1392.6017	3008.7696	0.0268	0.9777
HKYIG	41	-1383.9654	3009.1471	0.0222	0.9999
GTRG	44	-1380.8742	3020.6146	0.0001	1.0000
GTRI	44	-1382.6530	3024.1723	0.0000	1.0000
SYMG	41	-1391.7594	3024.7350	0.0000	1.0000
GTRIG	45	-1380.8031	3026.3558	0.0000	1.0000
SYMI	41	-1394.4292	3030.0746	0.0000	1.0000
SYMIG	42	-1391.7136	3030.5267	0.0000	1.0000
K2P	36	-1415.2148	3042.2292	0.0000	1.0000
HKY	39	-1406.5241	3042.4977	0.0000	1.0000
GTR	43	-1402.8227	3058.6283	0.0000	1.0000
SYM	40	-1414.3140	3063.9609	0.0000	1.0000
JC69G	36	-1436.4516	3084.7028	0.0000	1.0000
F81G	39	-1428.6986	3086.8467	0.0000	1.0000
JC69I	36	-1439.0693	3089.9381	0.0000	1.0000
JC69IG	37	-1436.4223	3090.5276	0.0000	1.0000
F81I	39	-1431.0472	3091.5440	0.0000	1.0000
F81IG	40	-1428.6670	3092.6669	0.0000	1.0000
JC69	35	-1457.5071	3120.9305	0.0000	1.0000
F81	38	-1449.5492	3122.6647	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/chr8_3325.phylip = 1 - 359;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3325.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/chr8_3325.phylip = 1 - 359;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3325.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/chr8_3325.phylip = 1 - 359;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_3325.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

