
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:39 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/chr5_10207.phylip" (19 taxa, 682 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
Minimum BIC  model: K2PG


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
HKYIG	41	-2331.2114	4749.8040	0.5801	0.5801
HKYG	40	-2332.9622	4751.0414	0.3125	0.8926
GTRIG	45	-2329.1266	4754.7627	0.0486	0.9412
GTRG	44	-2330.6489	4755.5145	0.0334	0.9746
HKYI	40	-2335.7804	4756.6779	0.0187	0.9932
K2PG	37	-2341.1599	4760.6863	0.0025	0.9957
GTRI	44	-2333.5173	4761.2513	0.0019	0.9976
K2PIG	38	-2340.5077	4761.6250	0.0016	0.9992
SYMG	41	-2338.5843	4764.5498	0.0004	0.9996
SYMIG	42	-2338.0055	4765.6635	0.0002	0.9998
K2PI	37	-2343.6958	4765.7581	0.0002	1.0000
SYMI	41	-2340.9749	4769.3310	0.0000	1.0000
HKY	39	-2373.8084	4830.4767	0.0000	1.0000
GTR	43	-2371.2518	4834.4346	0.0000	1.0000
K2P	36	-2382.6480	4841.4263	0.0000	1.0000
SYM	40	-2379.1877	4843.4924	0.0000	1.0000
F81G	39	-2395.6336	4874.1269	0.0000	1.0000
F81IG	40	-2395.1661	4875.4492	0.0000	1.0000
F81I	39	-2397.9435	4878.7468	0.0000	1.0000
JC69G	36	-2404.8092	4885.7487	0.0000	1.0000
JC69IG	37	-2404.3747	4887.1159	0.0000	1.0000
JC69I	36	-2406.9502	4890.0307	0.0000	1.0000
F81	38	-2435.5064	4951.6224	0.0000	1.0000
JC69	35	-2444.3374	4962.5757	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-2331.2114	4744.4227	0.5729	0.5729
HKYG	40	-2332.9622	4745.9244	0.2704	0.8433
GTRIG	45	-2329.1266	4748.2533	0.0844	0.9277
GTRG	44	-2330.6489	4749.2978	0.0501	0.9777
HKYI	40	-2335.7804	4751.5609	0.0161	0.9939
GTRI	44	-2333.5173	4755.0346	0.0028	0.9967
K2PG	37	-2341.1599	4756.3198	0.0015	0.9982
K2PIG	38	-2340.5077	4757.0153	0.0011	0.9993
SYMG	41	-2338.5843	4759.1685	0.0004	0.9996
SYMIG	42	-2338.0055	4760.0109	0.0002	0.9998
K2PI	37	-2343.6958	4761.3916	0.0001	1.0000
SYMI	41	-2340.9749	4763.9497	0.0000	1.0000
HKY	39	-2373.8084	4825.6169	0.0000	1.0000
GTR	43	-2371.2518	4828.5036	0.0000	1.0000
K2P	36	-2382.6480	4837.2961	0.0000	1.0000
SYM	40	-2379.1877	4838.3754	0.0000	1.0000
F81G	39	-2395.6336	4869.2671	0.0000	1.0000
F81IG	40	-2395.1661	4870.3322	0.0000	1.0000
F81I	39	-2397.9435	4873.8870	0.0000	1.0000
JC69G	36	-2404.8092	4881.6185	0.0000	1.0000
JC69IG	37	-2404.3747	4882.7494	0.0000	1.0000
JC69I	36	-2406.9502	4885.9005	0.0000	1.0000
F81	38	-2435.5064	4947.0127	0.0000	1.0000
JC69	35	-2444.3374	4958.6748	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2341.1599	4923.7459	0.7073	0.7073
HKYG	40	-2332.9622	4926.9256	0.1443	0.8515
K2PI	37	-2343.6958	4928.8177	0.0560	0.9075
K2PIG	38	-2340.5077	4928.9664	0.0520	0.9595
HKYIG	41	-2331.2114	4929.9489	0.0318	0.9914
HKYI	40	-2335.7804	4932.5621	0.0086	1.0000
SYMG	41	-2338.5843	4944.6947	0.0000	1.0000
GTRG	44	-2330.6489	4948.3991	0.0000	1.0000
SYMI	41	-2340.9749	4949.4759	0.0000	1.0000
SYMIG	42	-2338.0055	4950.0622	0.0000	1.0000
GTRIG	45	-2329.1266	4951.8796	0.0000	1.0000
GTRI	44	-2333.5173	4954.1359	0.0000	1.0000
K2P	36	-2382.6480	5000.1971	0.0000	1.0000
HKY	39	-2373.8084	5002.0930	0.0000	1.0000
SYM	40	-2379.1877	5019.3766	0.0000	1.0000
GTR	43	-2371.2518	5023.0798	0.0000	1.0000
JC69G	36	-2404.8092	5044.5195	0.0000	1.0000
F81G	39	-2395.6336	5045.7433	0.0000	1.0000
JC69I	36	-2406.9502	5048.8015	0.0000	1.0000
JC69IG	37	-2404.3747	5050.1755	0.0000	1.0000
F81I	39	-2397.9435	5050.3631	0.0000	1.0000
F81IG	40	-2395.1661	5051.3334	0.0000	1.0000
JC69	35	-2444.3374	5117.0508	0.0000	1.0000
F81	38	-2435.5064	5118.9638	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10207.phylip = 1 - 682;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10207.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10207.phylip = 1 - 682;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10207.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10207.phylip = 1 - 682;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10207.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

