
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:34 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/chr11_3253.phylip" (19 taxa, 518 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-1450.0693	2998.9098	0.5047	0.5047
GTRG	44	-1451.7110	2999.7940	0.3243	0.8290
GTRI	44	-1452.5053	3001.3827	0.1466	0.9756
HKYIG	41	-1458.6453	3006.5260	0.0112	0.9868
HKYG	40	-1460.0235	3006.9233	0.0092	0.9960
HKYI	40	-1460.8477	3008.5718	0.0040	1.0000
F81IG	40	-1478.1043	3043.0850	0.0000	1.0000
F81G	39	-1479.3096	3043.1464	0.0000	1.0000
SYMIG	42	-1475.8952	3043.3947	0.0000	1.0000
SYMG	41	-1477.1365	3043.5083	0.0000	1.0000
SYMI	41	-1477.7582	3044.7517	0.0000	1.0000
F81I	39	-1480.1168	3044.7607	0.0000	1.0000
K2PIG	38	-1482.2023	3046.5926	0.0000	1.0000
K2PG	37	-1483.5061	3046.8705	0.0000	1.0000
K2PI	37	-1484.2475	3048.3534	0.0000	1.0000
GTR	43	-1486.1061	3066.1954	0.0000	1.0000
HKY	39	-1492.2207	3068.9686	0.0000	1.0000
JC69G	36	-1500.5575	3078.6535	0.0000	1.0000
JC69IG	37	-1499.4368	3078.7319	0.0000	1.0000
JC69I	36	-1501.2899	3080.1182	0.0000	1.0000
F81	38	-1510.7564	3103.7007	0.0000	1.0000
SYM	40	-1510.6115	3108.0993	0.0000	1.0000
K2P	36	-1515.9671	3109.4728	0.0000	1.0000
JC69	35	-1532.2336	3139.6954	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1450.0693	2990.1386	0.5603	0.5603
GTRG	44	-1451.7110	2991.4219	0.2950	0.8553
GTRI	44	-1452.5053	2993.0106	0.1333	0.9885
HKYIG	41	-1458.6453	2999.2907	0.0058	0.9943
HKYG	40	-1460.0235	3000.0470	0.0040	0.9983
HKYI	40	-1460.8477	3001.6954	0.0017	1.0000
SYMIG	42	-1475.8952	3035.7904	0.0000	1.0000
F81IG	40	-1478.1043	3036.2087	0.0000	1.0000
SYMG	41	-1477.1365	3036.2730	0.0000	1.0000
F81G	39	-1479.3096	3036.6192	0.0000	1.0000
SYMI	41	-1477.7582	3037.5164	0.0000	1.0000
F81I	39	-1480.1168	3038.2335	0.0000	1.0000
K2PIG	38	-1482.2023	3040.4047	0.0000	1.0000
K2PG	37	-1483.5061	3041.0122	0.0000	1.0000
K2PI	37	-1484.2475	3042.4951	0.0000	1.0000
GTR	43	-1486.1061	3058.2123	0.0000	1.0000
HKY	39	-1492.2207	3062.4414	0.0000	1.0000
JC69IG	37	-1499.4368	3072.8735	0.0000	1.0000
JC69G	36	-1500.5575	3073.1151	0.0000	1.0000
JC69I	36	-1501.2899	3074.5798	0.0000	1.0000
F81	38	-1510.7564	3097.5128	0.0000	1.0000
SYM	40	-1510.6115	3101.2230	0.0000	1.0000
K2P	36	-1515.9671	3103.9343	0.0000	1.0000
JC69	35	-1532.2336	3134.4672	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1460.0235	3170.0460	0.6104	0.6104
HKYI	40	-1460.8477	3171.6944	0.2677	0.8780
HKYIG	41	-1458.6453	3173.5397	0.1064	0.9844
GTRG	44	-1451.7110	3178.4209	0.0093	0.9937
GTRI	44	-1452.5053	3180.0095	0.0042	0.9979
GTRIG	45	-1450.0693	3181.3875	0.0021	1.0000
K2PG	37	-1483.5061	3198.2613	0.0000	1.0000
K2PI	37	-1484.2475	3199.7442	0.0000	1.0000
K2PIG	38	-1482.2023	3201.9037	0.0000	1.0000
F81G	39	-1479.3096	3202.3682	0.0000	1.0000
F81I	39	-1480.1168	3203.9826	0.0000	1.0000
F81IG	40	-1478.1043	3206.2077	0.0000	1.0000
SYMG	41	-1477.1365	3210.5219	0.0000	1.0000
SYMI	41	-1477.7582	3211.7653	0.0000	1.0000
SYMIG	42	-1475.8952	3214.2894	0.0000	1.0000
JC69G	36	-1500.5575	3226.1142	0.0000	1.0000
JC69I	36	-1501.2899	3227.5789	0.0000	1.0000
HKY	39	-1492.2207	3228.1904	0.0000	1.0000
JC69IG	37	-1499.4368	3230.1226	0.0000	1.0000
GTR	43	-1486.1061	3240.9612	0.0000	1.0000
K2P	36	-1515.9671	3256.9334	0.0000	1.0000
F81	38	-1510.7564	3259.0118	0.0000	1.0000
SYM	40	-1510.6115	3271.2220	0.0000	1.0000
JC69	35	-1532.2336	3283.2163	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3253.phylip = 1 - 518;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3253.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3253.phylip = 1 - 518;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3253.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr11_3253.phylip = 1 - 518;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3253.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

