
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_32247.phylip" (19 taxa, 566 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	-1177.6017	2450.8041	0.4312	0.4312
HKYG	40	-1182.4355	2451.1185	0.3685	0.7997
GTRI	44	-1179.2705	2454.1418	0.0813	0.8810
GTRIG	45	-1178.4918	2454.9451	0.0544	0.9353
HKYI	40	-1184.6987	2455.6451	0.0383	0.9737
HKYIG	41	-1183.9117	2456.3960	0.0263	1.0000
HKY	39	-1194.5801	2473.0917	0.0000	1.0000
GTR	43	-1191.5446	2476.3382	0.0000	1.0000
F81I	39	-1206.5963	2497.1242	0.0000	1.0000
F81G	39	-1206.7134	2497.3583	0.0000	1.0000
F81IG	40	-1205.9159	2498.0795	0.0000	1.0000
K2PG	37	-1210.5841	2500.4940	0.0000	1.0000
SYMG	41	-1208.5562	2505.6849	0.0000	1.0000
K2PI	37	-1213.3246	2505.9750	0.0000	1.0000
K2PIG	38	-1212.5934	2506.8110	0.0000	1.0000
SYMI	41	-1210.9005	2510.3736	0.0000	1.0000
SYMIG	42	-1210.2084	2511.3231	0.0000	1.0000
F81	38	-1218.5322	2518.6887	0.0000	1.0000
K2P	36	-1222.8972	2522.8303	0.0000	1.0000
SYM	40	-1223.0389	2532.3255	0.0000	1.0000
JC69I	36	-1232.7520	2542.5399	0.0000	1.0000
JC69G	36	-1232.9004	2542.8367	0.0000	1.0000
JC69IG	37	-1232.0782	2543.4822	0.0000	1.0000
JC69	35	-1244.8863	2564.5273	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1177.6017	2443.2033	0.5389	0.5389
HKYG	40	-1182.4355	2444.8709	0.2341	0.7730
GTRI	44	-1179.2705	2446.5410	0.1016	0.8746
GTRIG	45	-1178.4918	2446.9835	0.0814	0.9560
HKYI	40	-1184.6987	2449.3975	0.0243	0.9803
HKYIG	41	-1183.9117	2449.8235	0.0197	1.0000
HKY	39	-1194.5801	2467.1602	0.0000	1.0000
GTR	43	-1191.5446	2469.0891	0.0000	1.0000
F81I	39	-1206.5963	2491.1926	0.0000	1.0000
F81G	39	-1206.7134	2491.4268	0.0000	1.0000
F81IG	40	-1205.9159	2491.8319	0.0000	1.0000
K2PG	37	-1210.5841	2495.1683	0.0000	1.0000
SYMG	41	-1208.5562	2499.1124	0.0000	1.0000
K2PI	37	-1213.3246	2500.6492	0.0000	1.0000
K2PIG	38	-1212.5934	2501.1868	0.0000	1.0000
SYMI	41	-1210.9005	2503.8011	0.0000	1.0000
SYMIG	42	-1210.2084	2504.4168	0.0000	1.0000
F81	38	-1218.5322	2513.0644	0.0000	1.0000
K2P	36	-1222.8972	2517.7944	0.0000	1.0000
SYM	40	-1223.0389	2526.0779	0.0000	1.0000
JC69I	36	-1232.7520	2537.5040	0.0000	1.0000
JC69G	36	-1232.9004	2537.8008	0.0000	1.0000
JC69IG	37	-1232.0782	2538.1564	0.0000	1.0000
JC69	35	-1244.8863	2559.7725	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1182.4355	2618.4147	0.8975	0.8975
HKYI	40	-1184.6987	2622.9412	0.0933	0.9908
HKYIG	41	-1183.9117	2627.7059	0.0086	0.9995
GTRG	44	-1177.6017	2634.1015	0.0004	0.9998
HKY	39	-1194.5801	2636.3653	0.0001	0.9999
GTRI	44	-1179.2705	2637.4392	0.0001	1.0000
GTRIG	45	-1178.4918	2642.2203	0.0000	1.0000
GTR	43	-1191.5446	2655.6487	0.0000	1.0000
K2PG	37	-1210.5841	2655.6962	0.0000	1.0000
F81I	39	-1206.5963	2660.3978	0.0000	1.0000
F81G	39	-1206.7134	2660.6319	0.0000	1.0000
K2PI	37	-1213.3246	2661.1772	0.0000	1.0000
F81IG	40	-1205.9159	2665.3756	0.0000	1.0000
K2PIG	38	-1212.5934	2666.0533	0.0000	1.0000
K2P	36	-1222.8972	2673.9838	0.0000	1.0000
SYMG	41	-1208.5562	2676.9947	0.0000	1.0000
F81	38	-1218.5322	2677.9310	0.0000	1.0000
SYMI	41	-1210.9005	2681.6834	0.0000	1.0000
SYMIG	42	-1210.2084	2686.6378	0.0000	1.0000
JC69I	36	-1232.7520	2693.6934	0.0000	1.0000
JC69G	36	-1232.9004	2693.9902	0.0000	1.0000
JC69IG	37	-1232.0782	2698.6844	0.0000	1.0000
SYM	40	-1223.0389	2699.6216	0.0000	1.0000
JC69	35	-1244.8863	2711.6233	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/chr1_32247.phylip = 1 - 566;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32247.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/chr1_32247.phylip = 1 - 566;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32247.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/chr1_32247.phylip = 1 - 566;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32247.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

