
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:26 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/chrZ_60.phylip" (19 taxa, 469 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	-1411.2223	2910.1082	0.4698	0.4698
HKYIG	41	-1410.7364	2911.5384	0.2298	0.6997
HKYI	40	-1412.4251	2912.5137	0.1411	0.8408
GTRG	44	-1408.0200	2913.3797	0.0915	0.9323
GTRIG	45	-1407.6225	2915.0323	0.0401	0.9724
GTRI	44	-1409.2173	2915.7742	0.0276	1.0000
F81G	39	-1426.2069	2937.6864	0.0000	1.0000
F81IG	40	-1425.8078	2939.2793	0.0000	1.0000
F81I	39	-1427.2230	2939.7187	0.0000	1.0000
K2PG	37	-1433.7630	2948.0504	0.0000	1.0000
K2PIG	38	-1433.1577	2949.2084	0.0000	1.0000
K2PI	37	-1434.9548	2950.4340	0.0000	1.0000
SYMG	41	-1432.1588	2954.3831	0.0000	1.0000
SYMIG	42	-1431.5395	2955.5580	0.0000	1.0000
HKY	39	-1435.6994	2956.6714	0.0000	1.0000
SYMI	41	-1433.3723	2956.8103	0.0000	1.0000
GTR	43	-1431.7901	2958.4837	0.0000	1.0000
JC69G	36	-1447.6410	2973.4487	0.0000	1.0000
JC69IG	37	-1447.1588	2974.8419	0.0000	1.0000
JC69I	36	-1448.7234	2975.6134	0.0000	1.0000
F81	38	-1450.7574	2984.4077	0.0000	1.0000
K2P	36	-1459.9453	2998.0573	0.0000	1.0000
SYM	40	-1458.1265	3003.9165	0.0000	1.0000
JC69	35	-1472.9624	3021.7447	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1411.2223	2902.4446	0.3661	0.3661
HKYIG	41	-1410.7364	2903.4728	0.2190	0.5851
GTRG	44	-1408.0200	2904.0401	0.1649	0.7500
HKYI	40	-1412.4251	2904.8502	0.1100	0.8599
GTRIG	45	-1407.6225	2905.2451	0.0903	0.9502
GTRI	44	-1409.2173	2906.4346	0.0498	1.0000
F81G	39	-1426.2069	2930.4137	0.0000	1.0000
F81IG	40	-1425.8078	2931.6157	0.0000	1.0000
F81I	39	-1427.2230	2932.4460	0.0000	1.0000
K2PG	37	-1433.7630	2941.5260	0.0000	1.0000
K2PIG	38	-1433.1577	2942.3153	0.0000	1.0000
K2PI	37	-1434.9548	2943.9096	0.0000	1.0000
SYMG	41	-1432.1588	2946.3175	0.0000	1.0000
SYMIG	42	-1431.5395	2947.0791	0.0000	1.0000
SYMI	41	-1433.3723	2948.7447	0.0000	1.0000
HKY	39	-1435.6994	2949.3987	0.0000	1.0000
GTR	43	-1431.7901	2949.5802	0.0000	1.0000
JC69G	36	-1447.6410	2967.2821	0.0000	1.0000
JC69IG	37	-1447.1588	2968.3175	0.0000	1.0000
JC69I	36	-1448.7234	2969.4467	0.0000	1.0000
F81	38	-1450.7574	2977.5147	0.0000	1.0000
K2P	36	-1459.9453	2991.8907	0.0000	1.0000
SYM	40	-1458.1265	2996.2530	0.0000	1.0000
JC69	35	-1472.9624	3015.9249	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1411.2223	3068.4687	0.7270	0.7270
HKYI	40	-1412.4251	3070.8743	0.2183	0.9453
HKYIG	41	-1410.7364	3073.6475	0.0546	0.9999
GTRG	44	-1408.0200	3086.6666	0.0001	1.0000
GTRI	44	-1409.2173	3089.0611	0.0000	1.0000
GTRIG	45	-1407.6225	3092.0222	0.0000	1.0000
F81G	39	-1426.2069	3092.2872	0.0000	1.0000
F81I	39	-1427.2230	3094.3195	0.0000	1.0000
K2PG	37	-1433.7630	3095.0983	0.0000	1.0000
K2PI	37	-1434.9548	3097.4819	0.0000	1.0000
F81IG	40	-1425.8078	3097.6398	0.0000	1.0000
K2PIG	38	-1433.1577	3100.0382	0.0000	1.0000
HKY	39	-1435.6994	3111.2722	0.0000	1.0000
SYMG	41	-1432.1588	3116.4922	0.0000	1.0000
JC69G	36	-1447.6410	3116.7038	0.0000	1.0000
JC69I	36	-1448.7234	3118.8684	0.0000	1.0000
SYMI	41	-1433.3723	3118.9194	0.0000	1.0000
SYMIG	42	-1431.5395	3121.4044	0.0000	1.0000
JC69IG	37	-1447.1588	3121.8898	0.0000	1.0000
GTR	43	-1431.7901	3128.0561	0.0000	1.0000
F81	38	-1450.7574	3135.2376	0.0000	1.0000
K2P	36	-1459.9453	3141.3124	0.0000	1.0000
JC69	35	-1472.9624	3161.1960	0.0000	1.0000
SYM	40	-1458.1265	3162.2771	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/chrZ_60.phylip = 1 - 469;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_60.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/chrZ_60.phylip = 1 - 469;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_60.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/chrZ_60.phylip = 1 - 469;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_60.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

