
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:46 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/chr2_25851.phylip" (19 taxa, 725 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-2555.2793	5195.3539	0.3739	0.3739
GTRG	44	-2551.0164	5195.8564	0.2909	0.6648
HKYIG	41	-2555.2774	5197.5973	0.1218	0.7866
GTRIG	45	-2551.0104	5198.1180	0.0939	0.8805
HKYI	40	-2556.9479	5198.6912	0.0705	0.9510
GTRI	44	-2552.7974	5199.4183	0.0490	1.0000
K2PG	37	-2571.2680	5220.6292	0.0000	1.0000
HKY	39	-2569.4282	5221.4112	0.0000	1.0000
K2PIG	38	-2571.2665	5222.8536	0.0000	1.0000
GTR	43	-2565.8557	5223.2680	0.0000	1.0000
K2PI	37	-2573.0582	5224.2095	0.0000	1.0000
SYMG	41	-2568.8966	5224.8356	0.0000	1.0000
SYMIG	42	-2568.8956	5227.0874	0.0000	1.0000
SYMI	41	-2570.8584	5228.7593	0.0000	1.0000
K2P	36	-2585.6604	5247.1929	0.0000	1.0000
SYM	40	-2583.7579	5252.3111	0.0000	1.0000
F81G	39	-2628.3915	5339.3378	0.0000	1.0000
F81IG	40	-2628.3940	5341.5834	0.0000	1.0000
F81I	39	-2629.8412	5342.2371	0.0000	1.0000
JC69G	36	-2641.1275	5358.1270	0.0000	1.0000
JC69IG	37	-2641.1336	5360.3604	0.0000	1.0000
JC69I	36	-2642.6665	5361.2052	0.0000	1.0000
F81	38	-2640.8627	5362.0461	0.0000	1.0000
JC69	35	-2653.8896	5381.4367	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2551.0164	5190.0328	0.3655	0.3655
HKYG	40	-2555.2793	5190.5586	0.2810	0.6466
GTRIG	45	-2551.0104	5192.0208	0.1353	0.7819
HKYIG	41	-2555.2774	5192.5548	0.1036	0.8854
GTRI	44	-2552.7974	5193.5948	0.0616	0.9470
HKYI	40	-2556.9479	5193.8959	0.0530	1.0000
K2PG	37	-2571.2680	5216.5360	0.0000	1.0000
HKY	39	-2569.4282	5216.8565	0.0000	1.0000
GTR	43	-2565.8557	5217.7114	0.0000	1.0000
K2PIG	38	-2571.2665	5218.5329	0.0000	1.0000
SYMG	41	-2568.8966	5219.7932	0.0000	1.0000
K2PI	37	-2573.0582	5220.1164	0.0000	1.0000
SYMIG	42	-2568.8956	5221.7912	0.0000	1.0000
SYMI	41	-2570.8584	5223.7168	0.0000	1.0000
K2P	36	-2585.6604	5243.3208	0.0000	1.0000
SYM	40	-2583.7579	5247.5158	0.0000	1.0000
F81G	39	-2628.3915	5334.7830	0.0000	1.0000
F81IG	40	-2628.3940	5336.7881	0.0000	1.0000
F81I	39	-2629.8412	5337.6823	0.0000	1.0000
JC69G	36	-2641.1275	5354.2549	0.0000	1.0000
JC69IG	37	-2641.1336	5356.2673	0.0000	1.0000
JC69I	36	-2642.6665	5357.3331	0.0000	1.0000
F81	38	-2640.8627	5357.7254	0.0000	1.0000
JC69	35	-2653.8896	5377.7792	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2555.2793	5374.0054	0.8140	0.8140
HKYI	40	-2556.9479	5377.3427	0.1534	0.9674
HKYIG	41	-2555.2774	5380.5879	0.0303	0.9977
K2PG	37	-2571.2680	5386.2244	0.0018	0.9995
K2PI	37	-2573.0582	5389.8047	0.0003	0.9998
GTRG	44	-2551.0164	5391.8244	0.0001	0.9999
K2PIG	38	-2571.2665	5392.8075	0.0001	1.0000
GTRI	44	-2552.7974	5395.3864	0.0000	1.0000
HKY	39	-2569.4282	5395.7172	0.0000	1.0000
GTRIG	45	-2551.0104	5398.3985	0.0000	1.0000
SYMG	41	-2568.8966	5407.8262	0.0000	1.0000
K2P	36	-2585.6604	5408.4230	0.0000	1.0000
SYMI	41	-2570.8584	5411.7499	0.0000	1.0000
SYMIG	42	-2568.8956	5414.4104	0.0000	1.0000
GTR	43	-2565.8557	5414.9168	0.0000	1.0000
SYM	40	-2583.7579	5430.9626	0.0000	1.0000
F81G	39	-2628.3915	5513.6437	0.0000	1.0000
F81I	39	-2629.8412	5516.5430	0.0000	1.0000
JC69G	36	-2641.1275	5519.3571	0.0000	1.0000
F81IG	40	-2628.3940	5520.2350	0.0000	1.0000
JC69I	36	-2642.6665	5522.4353	0.0000	1.0000
JC69IG	37	-2641.1336	5525.9556	0.0000	1.0000
F81	38	-2640.8627	5531.9999	0.0000	1.0000
JC69	35	-2653.8896	5538.2952	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/chr2_25851.phylip = 1 - 725;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25851.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/chr2_25851.phylip = 1 - 725;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25851.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25851.phylip = 1 - 725;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_25851.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

