
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:08 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_7188.phylip" (19 taxa, 705 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	-2405.0888	4904.1777	0.7199	0.7199
GTRIG	45	-2405.1161	4906.5144	0.2238	0.9437
GTRG	44	-2407.6439	4909.2878	0.0559	0.9996
HKYI	40	-2417.4422	4919.8242	0.0003	0.9999
HKYIG	41	-2417.4773	4922.1492	0.0001	1.0000
HKYG	40	-2419.8453	4924.6304	0.0000	1.0000
GTR	43	-2431.1247	4953.9741	0.0000	1.0000
HKY	39	-2441.1793	4965.0504	0.0000	1.0000
K2PI	37	-2472.9375	5024.0910	0.0000	1.0000
SYMI	41	-2468.8534	5024.9014	0.0000	1.0000
K2PIG	38	-2472.9679	5026.3862	0.0000	1.0000
SYMIG	42	-2468.8952	5027.2466	0.0000	1.0000
K2PG	37	-2474.7715	5027.7588	0.0000	1.0000
SYMG	41	-2471.2410	5029.6765	0.0000	1.0000
F81I	39	-2482.2106	5047.1129	0.0000	1.0000
F81IG	40	-2482.2407	5049.4211	0.0000	1.0000
F81G	39	-2483.9562	5050.6042	0.0000	1.0000
K2P	36	-2496.0385	5068.0651	0.0000	1.0000
SYM	40	-2493.0333	5071.0064	0.0000	1.0000
F81	38	-2502.3714	5085.1932	0.0000	1.0000
JC69I	36	-2524.8435	5125.6750	0.0000	1.0000
JC69IG	37	-2524.8764	5127.9688	0.0000	1.0000
JC69G	36	-2526.6426	5129.2732	0.0000	1.0000
JC69	35	-2545.4795	5164.7259	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-2405.0888	4898.1777	0.6964	0.6964
GTRIG	45	-2405.1161	4900.2321	0.2493	0.9457
GTRG	44	-2407.6439	4903.2878	0.0541	0.9998
HKYI	40	-2417.4422	4914.8844	0.0002	0.9999
HKYIG	41	-2417.4773	4916.9546	0.0001	1.0000
HKYG	40	-2419.8453	4919.6906	0.0000	1.0000
GTR	43	-2431.1247	4948.2494	0.0000	1.0000
HKY	39	-2441.1793	4960.3587	0.0000	1.0000
SYMI	41	-2468.8534	5019.7069	0.0000	1.0000
K2PI	37	-2472.9375	5019.8751	0.0000	1.0000
SYMIG	42	-2468.8952	5021.7904	0.0000	1.0000
K2PIG	38	-2472.9679	5021.9357	0.0000	1.0000
K2PG	37	-2474.7715	5023.5429	0.0000	1.0000
SYMG	41	-2471.2410	5024.4819	0.0000	1.0000
F81I	39	-2482.2106	5042.4211	0.0000	1.0000
F81IG	40	-2482.2407	5044.4813	0.0000	1.0000
F81G	39	-2483.9562	5045.9125	0.0000	1.0000
K2P	36	-2496.0385	5064.0770	0.0000	1.0000
SYM	40	-2493.0333	5066.0667	0.0000	1.0000
F81	38	-2502.3714	5080.7428	0.0000	1.0000
JC69I	36	-2524.8435	5121.6870	0.0000	1.0000
JC69IG	37	-2524.8764	5123.7529	0.0000	1.0000
JC69G	36	-2526.6426	5125.2852	0.0000	1.0000
JC69	35	-2545.4795	5160.9591	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-2417.4422	5097.2124	0.6074	0.6074
GTRI	44	-2405.0888	5098.7384	0.2832	0.8906
HKYG	40	-2419.8453	5102.0186	0.0549	0.9455
HKYIG	41	-2417.4773	5103.8407	0.0221	0.9676
GTRG	44	-2407.6439	5103.8485	0.0220	0.9896
GTRIG	45	-2405.1161	5105.3510	0.0104	1.0000
HKY	39	-2441.1793	5138.1284	0.0000	1.0000
GTR	43	-2431.1247	5144.2519	0.0000	1.0000
K2PI	37	-2472.9375	5188.5284	0.0000	1.0000
K2PG	37	-2474.7715	5192.1962	0.0000	1.0000
K2PIG	38	-2472.9679	5195.1472	0.0000	1.0000
SYMI	41	-2468.8534	5206.5930	0.0000	1.0000
SYMG	41	-2471.2410	5211.3680	0.0000	1.0000
SYMIG	42	-2468.8952	5213.2347	0.0000	1.0000
F81I	39	-2482.2106	5220.1909	0.0000	1.0000
F81G	39	-2483.9562	5223.6822	0.0000	1.0000
F81IG	40	-2482.2407	5226.8092	0.0000	1.0000
K2P	36	-2496.0385	5228.1722	0.0000	1.0000
SYM	40	-2493.0333	5248.3946	0.0000	1.0000
F81	38	-2502.3714	5253.9543	0.0000	1.0000
JC69I	36	-2524.8435	5285.7821	0.0000	1.0000
JC69G	36	-2526.6426	5289.3803	0.0000	1.0000
JC69IG	37	-2524.8764	5292.4062	0.0000	1.0000
JC69	35	-2545.4795	5320.4960	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/chr9_7188.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7188.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/chr9_7188.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7188.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/chr9_7188.phylip = 1 - 705;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7188.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

