
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:27 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/chr9_3289.phylip" (19 taxa, 398 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	-1342.4771	2774.1419	0.4870	0.4870
HKYI	40	-1342.8771	2774.9418	0.3265	0.8134
HKYIG	41	-1342.3508	2776.3758	0.1594	0.9728
GTRG	44	-1340.9541	2781.1264	0.0148	0.9876
GTRI	44	-1341.6155	2782.4491	0.0076	0.9953
GTRIG	45	-1340.8292	2783.4198	0.0047	1.0000
F81G	39	-1357.0070	2800.7291	0.0000	1.0000
F81I	39	-1357.4639	2801.6428	0.0000	1.0000
F81IG	40	-1356.9156	2803.0188	0.0000	1.0000
HKY	39	-1358.7209	2804.1569	0.0000	1.0000
K2PG	37	-1361.7377	2805.2865	0.0000	1.0000
K2PI	37	-1362.3567	2806.5245	0.0000	1.0000
K2PIG	38	-1361.6527	2807.5617	0.0000	1.0000
SYMG	41	-1358.2605	2808.1952	0.0000	1.0000
SYMI	41	-1359.2228	2810.1198	0.0000	1.0000
SYMIG	42	-1358.1521	2810.4788	0.0000	1.0000
GTR	43	-1356.9248	2810.5389	0.0000	1.0000
JC69G	36	-1373.5435	2826.4665	0.0000	1.0000
JC69I	36	-1374.1052	2827.5899	0.0000	1.0000
F81	38	-1372.0804	2828.4171	0.0000	1.0000
JC69IG	37	-1373.4674	2828.7460	0.0000	1.0000
K2P	36	-1376.0984	2831.5763	0.0000	1.0000
SYM	40	-1372.0054	2833.1984	0.0000	1.0000
JC69	35	-1387.6462	2852.2538	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1342.4771	2764.9542	0.4444	0.4444
HKYI	40	-1342.8771	2765.7541	0.2979	0.7423
HKYIG	41	-1342.3508	2766.7016	0.1855	0.9278
GTRG	44	-1340.9541	2769.9083	0.0373	0.9652
GTRI	44	-1341.6155	2771.2310	0.0193	0.9844
GTRIG	45	-1340.8292	2771.6584	0.0156	1.0000
F81G	39	-1357.0070	2792.0140	0.0000	1.0000
F81I	39	-1357.4639	2792.9278	0.0000	1.0000
F81IG	40	-1356.9156	2793.8311	0.0000	1.0000
HKY	39	-1358.7209	2795.4418	0.0000	1.0000
K2PG	37	-1361.7377	2797.4753	0.0000	1.0000
SYMG	41	-1358.2605	2798.5211	0.0000	1.0000
K2PI	37	-1362.3567	2798.7134	0.0000	1.0000
K2PIG	38	-1361.6527	2799.3054	0.0000	1.0000
GTR	43	-1356.9248	2799.8496	0.0000	1.0000
SYMIG	42	-1358.1521	2800.3042	0.0000	1.0000
SYMI	41	-1359.2228	2800.4456	0.0000	1.0000
JC69G	36	-1373.5435	2819.0870	0.0000	1.0000
F81	38	-1372.0804	2820.1608	0.0000	1.0000
JC69I	36	-1374.1052	2820.2104	0.0000	1.0000
JC69IG	37	-1373.4674	2820.9349	0.0000	1.0000
SYM	40	-1372.0054	2824.0107	0.0000	1.0000
K2P	36	-1376.0984	2824.1968	0.0000	1.0000
JC69	35	-1387.6462	2845.2925	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1342.4771	2924.4123	0.5789	0.5789
HKYI	40	-1342.8771	2925.2122	0.3881	0.9670
HKYIG	41	-1342.3508	2930.1462	0.0329	0.9999
K2PG	37	-1361.7377	2944.9741	0.0000	1.0000
GTRG	44	-1340.9541	2945.3121	0.0000	1.0000
K2PI	37	-1362.3567	2946.2121	0.0000	1.0000
GTRI	44	-1341.6155	2946.6349	0.0000	1.0000
F81G	39	-1357.0070	2947.4857	0.0000	1.0000
F81I	39	-1357.4639	2948.3994	0.0000	1.0000
K2PIG	38	-1361.6527	2950.7906	0.0000	1.0000
HKY	39	-1358.7209	2950.9134	0.0000	1.0000
GTRIG	45	-1340.8292	2951.0487	0.0000	1.0000
F81IG	40	-1356.9156	2953.2892	0.0000	1.0000
SYMG	41	-1358.2605	2961.9656	0.0000	1.0000
JC69G	36	-1373.5435	2962.5993	0.0000	1.0000
JC69I	36	-1374.1052	2963.7227	0.0000	1.0000
SYMI	41	-1359.2228	2963.8902	0.0000	1.0000
K2P	36	-1376.0984	2967.7091	0.0000	1.0000
SYMIG	42	-1358.1521	2967.7352	0.0000	1.0000
JC69IG	37	-1373.4674	2968.4336	0.0000	1.0000
GTR	43	-1356.9248	2971.2671	0.0000	1.0000
F81	38	-1372.0804	2971.6460	0.0000	1.0000
SYM	40	-1372.0054	2983.4688	0.0000	1.0000
JC69	35	-1387.6462	2984.8183	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/chr9_3289.phylip = 1 - 398;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_3289.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/chr9_3289.phylip = 1 - 398;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_3289.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/chr9_3289.phylip = 1 - 398;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_3289.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

