
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:49 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_11804.phylip" (19 taxa, 485 characters)

Minimum AIC  model: HKYG
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	-1319.2215	2725.8304	0.4011	0.4011
HKYI	40	-1319.8439	2727.0751	0.2153	0.6164
GTRG	44	-1315.4734	2727.9468	0.1392	0.7556
HKYIG	41	-1319.1689	2728.1121	0.1282	0.8838
GTRI	44	-1316.1402	2729.2804	0.0715	0.9553
GTRIG	45	-1315.4259	2730.2823	0.0433	0.9986
HKY	39	-1326.4735	2737.9583	0.0009	0.9995
GTR	43	-1322.3303	2739.2411	0.0005	1.0000
K2PG	37	-1334.8681	2750.0270	0.0000	1.0000
K2PI	37	-1335.5322	2751.3552	0.0000	1.0000
K2PIG	38	-1334.8159	2752.2775	0.0000	1.0000
SYMG	41	-1333.8799	2757.5340	0.0000	1.0000
SYMI	41	-1334.5412	2758.8566	0.0000	1.0000
SYMIG	42	-1333.8382	2759.8484	0.0000	1.0000
K2P	36	-1341.7735	2761.4934	0.0000	1.0000
SYM	40	-1340.3694	2768.1263	0.0000	1.0000
F81G	39	-1342.4495	2769.9103	0.0000	1.0000
F81I	39	-1343.0605	2771.1323	0.0000	1.0000
F81IG	40	-1343.1915	2773.7703	0.0000	1.0000
F81	38	-1348.9810	2780.6077	0.0000	1.0000
JC69G	36	-1356.6141	2791.1747	0.0000	1.0000
JC69I	36	-1357.2446	2792.4356	0.0000	1.0000
JC69IG	37	-1356.5697	2793.4303	0.0000	1.0000
JC69	35	-1363.3203	2802.2530	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1319.2215	2718.4430	0.2937	0.2937
GTRG	44	-1315.4734	2718.9468	0.2283	0.5220
HKYI	40	-1319.8439	2719.6877	0.1576	0.6796
GTRI	44	-1316.1402	2720.2804	0.1172	0.7968
HKYIG	41	-1319.1689	2720.3378	0.1139	0.9107
GTRIG	45	-1315.4259	2720.8517	0.0881	0.9988
GTR	43	-1322.3303	2730.6606	0.0007	0.9994
HKY	39	-1326.4735	2730.9470	0.0006	1.0000
K2PG	37	-1334.8681	2743.7362	0.0000	1.0000
K2PI	37	-1335.5322	2745.0644	0.0000	1.0000
K2PIG	38	-1334.8159	2745.6317	0.0000	1.0000
SYMG	41	-1333.8799	2749.7597	0.0000	1.0000
SYMI	41	-1334.5412	2751.0823	0.0000	1.0000
SYMIG	42	-1333.8382	2751.6765	0.0000	1.0000
K2P	36	-1341.7735	2755.5470	0.0000	1.0000
SYM	40	-1340.3694	2760.7389	0.0000	1.0000
F81G	39	-1342.4495	2762.8991	0.0000	1.0000
F81I	39	-1343.0605	2764.1211	0.0000	1.0000
F81IG	40	-1343.1915	2766.3829	0.0000	1.0000
F81	38	-1348.9810	2773.9620	0.0000	1.0000
JC69G	36	-1356.6141	2785.2283	0.0000	1.0000
JC69I	36	-1357.2446	2786.4891	0.0000	1.0000
JC69IG	37	-1356.5697	2787.1395	0.0000	1.0000
JC69	35	-1363.3203	2796.6405	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1319.2215	2885.8090	0.6238	0.6238
HKYI	40	-1319.8439	2887.0537	0.3348	0.9585
HKYIG	41	-1319.1689	2891.8879	0.0299	0.9884
HKY	39	-1326.4735	2894.1288	0.0097	0.9981
K2PG	37	-1334.8681	2898.5497	0.0011	0.9992
K2PI	37	-1335.5322	2899.8779	0.0005	0.9997
GTRG	44	-1315.4734	2903.0494	0.0001	0.9999
GTRI	44	-1316.1402	2904.3830	0.0001	0.9999
K2PIG	38	-1334.8159	2904.6294	0.0001	1.0000
K2P	36	-1341.7735	2906.1763	0.0000	1.0000
GTRIG	45	-1315.4259	2909.1384	0.0000	1.0000
GTR	43	-1322.3303	2910.5790	0.0000	1.0000
SYMG	41	-1333.8799	2921.3098	0.0000	1.0000
SYMI	41	-1334.5412	2922.6324	0.0000	1.0000
F81G	39	-1342.4495	2926.0809	0.0000	1.0000
F81I	39	-1343.0605	2927.3029	0.0000	1.0000
SYMIG	42	-1333.8382	2927.4107	0.0000	1.0000
SYM	40	-1340.3694	2928.1049	0.0000	1.0000
F81	38	-1348.9810	2932.9597	0.0000	1.0000
F81IG	40	-1343.1915	2933.7489	0.0000	1.0000
JC69G	36	-1356.6141	2935.8576	0.0000	1.0000
JC69I	36	-1357.2446	2937.1185	0.0000	1.0000
JC69IG	37	-1356.5697	2941.9530	0.0000	1.0000
JC69	35	-1363.3203	2943.0857	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/chr2_11804.phylip = 1 - 485;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11804.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/chr2_11804.phylip = 1 - 485;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11804.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_11804.phylip = 1 - 485;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_11804.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

