
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:02 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_7982.phylip" (19 taxa, 706 characters)

Minimum AIC  model: GTRG
Minimum AICc model: HKYG
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
HKYG	40	-2373.1381	4831.2085	0.3164	0.3164
HKYIG	41	-2372.3054	4831.7976	0.2356	0.5520
GTRG	44	-2368.9183	4831.8275	0.2321	0.7841
GTRIG	45	-2368.1823	4832.6372	0.1549	0.9390
HKYI	40	-2375.3406	4835.6135	0.0350	0.9740
GTRI	44	-2371.1647	4836.3204	0.0246	0.9985
K2PG	37	-2382.5596	4843.3287	0.0007	0.9993
K2PIG	38	-2381.7598	4843.9635	0.0005	0.9998
K2PI	37	-2384.3705	4846.9505	0.0001	0.9999
SYMG	41	-2380.7971	4848.7810	0.0000	1.0000
SYMIG	42	-2380.0480	4849.5439	0.0000	1.0000
SYMI	41	-2382.4859	4852.1586	0.0000	1.0000
HKY	39	-2410.2601	4903.2050	0.0000	1.0000
GTR	43	-2406.2535	4904.2230	0.0000	1.0000
K2P	36	-2419.6212	4915.2244	0.0000	1.0000
SYM	40	-2417.7825	4920.4974	0.0000	1.0000
F81G	39	-2427.6257	4937.9362	0.0000	1.0000
F81IG	40	-2426.9728	4938.8779	0.0000	1.0000
F81I	39	-2429.3636	4941.4119	0.0000	1.0000
JC69G	36	-2436.4329	4948.8479	0.0000	1.0000
JC69IG	37	-2435.7858	4949.7812	0.0000	1.0000
JC69I	36	-2438.0769	4952.1358	0.0000	1.0000
F81	38	-2462.9545	5006.3527	0.0000	1.0000
JC69	35	-2471.7586	5017.2783	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2368.9183	4825.8365	0.2901	0.2901
HKYG	40	-2373.1381	4826.2762	0.2329	0.5230
GTRIG	45	-2368.1823	4826.3645	0.2228	0.7458
HKYIG	41	-2372.3054	4826.6109	0.1970	0.9427
GTRI	44	-2371.1647	4830.3295	0.0307	0.9734
HKYI	40	-2375.3406	4830.6811	0.0257	0.9992
K2PG	37	-2382.5596	4839.1192	0.0004	0.9995
K2PIG	38	-2381.7598	4839.5197	0.0003	0.9999
K2PI	37	-2384.3705	4842.7409	0.0001	0.9999
SYMG	41	-2380.7971	4843.5943	0.0000	1.0000
SYMIG	42	-2380.0480	4844.0960	0.0000	1.0000
SYMI	41	-2382.4859	4846.9718	0.0000	1.0000
GTR	43	-2406.2535	4898.5070	0.0000	1.0000
HKY	39	-2410.2601	4898.5203	0.0000	1.0000
K2P	36	-2419.6212	4911.2423	0.0000	1.0000
SYM	40	-2417.7825	4915.5651	0.0000	1.0000
F81G	39	-2427.6257	4933.2515	0.0000	1.0000
F81IG	40	-2426.9728	4933.9456	0.0000	1.0000
F81I	39	-2429.3636	4936.7272	0.0000	1.0000
JC69G	36	-2436.4329	4944.8659	0.0000	1.0000
JC69IG	37	-2435.7858	4945.5716	0.0000	1.0000
JC69I	36	-2438.0769	4948.1537	0.0000	1.0000
F81	38	-2462.9545	5001.9090	0.0000	1.0000
JC69	35	-2471.7586	5013.5171	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-2382.5596	5007.8249	0.4913	0.4913
HKYG	40	-2373.1381	5008.6608	0.3235	0.8147
K2PI	37	-2384.3705	5011.4467	0.0803	0.8951
K2PIG	38	-2381.7598	5012.7851	0.0411	0.9362
HKYI	40	-2375.3406	5013.0657	0.0358	0.9719
HKYIG	41	-2372.3054	5013.5551	0.0280	0.9999
GTRG	44	-2368.9183	5026.4596	0.0000	1.0000
SYMG	41	-2380.7971	5030.5385	0.0000	1.0000
GTRI	44	-2371.1647	5030.9526	0.0000	1.0000
GTRIG	45	-2368.1823	5031.5472	0.0000	1.0000
SYMI	41	-2382.4859	5033.9161	0.0000	1.0000
SYMIG	42	-2380.0480	5035.5998	0.0000	1.0000
K2P	36	-2419.6212	5075.3885	0.0000	1.0000
HKY	39	-2410.2601	5076.3453	0.0000	1.0000
GTR	43	-2406.2535	5094.5704	0.0000	1.0000
SYM	40	-2417.7825	5097.9497	0.0000	1.0000
JC69G	36	-2436.4329	5109.0120	0.0000	1.0000
F81G	39	-2427.6257	5111.0765	0.0000	1.0000
JC69I	36	-2438.0769	5112.2999	0.0000	1.0000
JC69IG	37	-2435.7858	5114.2774	0.0000	1.0000
F81I	39	-2429.3636	5114.5522	0.0000	1.0000
F81IG	40	-2426.9728	5116.3302	0.0000	1.0000
JC69	35	-2471.7586	5173.1037	0.0000	1.0000
F81	38	-2462.9545	5175.1743	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7982.phylip = 1 - 706;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7982.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 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) 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_7982.phylip = 1 - 706;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7982.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7982.phylip = 1 - 706;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_7982.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

