
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:04 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_5297.phylip" (19 taxa, 450 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


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
GTRI	44	-1201.0954	2499.9685	0.7375	0.7375
GTRG	44	-1202.3874	2502.5526	0.2026	0.9401
GTRIG	45	-1202.3873	2505.0221	0.0589	0.9991
HKYI	40	-1212.9931	2514.0058	0.0007	0.9997
HKYG	40	-1214.1009	2516.2213	0.0002	0.9999
HKYIG	41	-1214.1008	2518.6428	0.0001	1.0000
GTR	43	-1214.9328	2525.1859	0.0000	1.0000
HKY	39	-1226.7441	2539.0980	0.0000	1.0000
F81I	39	-1240.5553	2566.7204	0.0000	1.0000
F81G	39	-1241.4672	2568.5441	0.0000	1.0000
F81IG	40	-1241.4671	2570.9539	0.0000	1.0000
K2PI	37	-1254.3151	2589.4554	0.0000	1.0000
SYMI	41	-1250.0625	2590.5661	0.0000	1.0000
K2PG	37	-1255.0280	2590.8813	0.0000	1.0000
SYMG	41	-1250.9685	2592.3781	0.0000	1.0000
F81	38	-1254.6168	2592.4453	0.0000	1.0000
K2PIG	38	-1255.0280	2593.2677	0.0000	1.0000
SYMIG	42	-1250.9683	2594.8114	0.0000	1.0000
SYM	40	-1264.4159	2616.8513	0.0000	1.0000
K2P	36	-1269.8174	2618.0851	0.0000	1.0000
JC69I	36	-1276.1673	2630.7849	0.0000	1.0000
JC69G	36	-1276.8920	2632.2343	0.0000	1.0000
JC69IG	37	-1276.8918	2634.6089	0.0000	1.0000
JC69	35	-1291.2217	2658.5304	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1201.0954	2490.1907	0.7266	0.7266
GTRG	44	-1202.3874	2492.7748	0.1996	0.9262
GTRIG	45	-1202.3873	2494.7746	0.0734	0.9996
HKYI	40	-1212.9931	2505.9862	0.0003	0.9999
HKYG	40	-1214.1009	2508.2017	0.0001	1.0000
HKYIG	41	-1214.1008	2510.2016	0.0000	1.0000
GTR	43	-1214.9328	2515.8657	0.0000	1.0000
HKY	39	-1226.7441	2531.4883	0.0000	1.0000
F81I	39	-1240.5553	2559.1106	0.0000	1.0000
F81G	39	-1241.4672	2560.9343	0.0000	1.0000
F81IG	40	-1241.4671	2562.9343	0.0000	1.0000
SYMI	41	-1250.0625	2582.1249	0.0000	1.0000
K2PI	37	-1254.3151	2582.6301	0.0000	1.0000
SYMG	41	-1250.9685	2583.9369	0.0000	1.0000
K2PG	37	-1255.0280	2584.0560	0.0000	1.0000
F81	38	-1254.6168	2585.2336	0.0000	1.0000
SYMIG	42	-1250.9683	2585.9367	0.0000	1.0000
K2PIG	38	-1255.0280	2586.0560	0.0000	1.0000
SYM	40	-1264.4159	2608.8317	0.0000	1.0000
K2P	36	-1269.8174	2611.6347	0.0000	1.0000
JC69I	36	-1276.1673	2624.3345	0.0000	1.0000
JC69G	36	-1276.8920	2625.7839	0.0000	1.0000
JC69IG	37	-1276.8918	2627.7837	0.0000	1.0000
JC69	35	-1291.2217	2652.4434	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1212.9931	2670.3561	0.4385	0.4385
GTRI	44	-1201.0954	2670.9976	0.3182	0.7568
HKYG	40	-1214.1009	2672.5716	0.1449	0.9016
GTRG	44	-1202.3874	2673.5817	0.0874	0.9890
HKYIG	41	-1214.1008	2678.6808	0.0068	0.9959
GTRIG	45	-1202.3873	2679.6907	0.0041	1.0000
HKY	39	-1226.7441	2691.7489	0.0000	1.0000
GTR	43	-1214.9328	2692.5633	0.0000	1.0000
F81I	39	-1240.5553	2719.3713	0.0000	1.0000
F81G	39	-1241.4672	2721.1950	0.0000	1.0000
F81IG	40	-1241.4671	2727.3042	0.0000	1.0000
K2PI	37	-1254.3151	2734.6723	0.0000	1.0000
K2PG	37	-1255.0280	2736.0982	0.0000	1.0000
F81	38	-1254.6168	2741.3850	0.0000	1.0000
K2PIG	38	-1255.0280	2742.2074	0.0000	1.0000
SYMI	41	-1250.0625	2750.6041	0.0000	1.0000
SYMG	41	-1250.9685	2752.4161	0.0000	1.0000
SYMIG	42	-1250.9683	2758.5251	0.0000	1.0000
K2P	36	-1269.8174	2759.5676	0.0000	1.0000
JC69I	36	-1276.1673	2772.2675	0.0000	1.0000
SYM	40	-1264.4159	2773.2016	0.0000	1.0000
JC69G	36	-1276.8920	2773.7169	0.0000	1.0000
JC69IG	37	-1276.8918	2779.8258	0.0000	1.0000
JC69	35	-1291.2217	2796.2671	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5297.phylip = 1 - 450;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5297.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5297.phylip = 1 - 450;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5297.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5297.phylip = 1 - 450;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5297.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

