
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:42 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/chr4_7557.phylip" (19 taxa, 557 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-2921.9406	5939.6156	0.6948	0.6948
GTRIG	45	-2921.8830	5941.8678	0.2253	0.9202
GTRI	44	-2924.2249	5944.1842	0.0708	0.9909
HKYG	40	-2931.3753	5949.1072	0.0060	0.9970
HKYIG	41	-2931.3291	5951.3455	0.0020	0.9989
HKYI	40	-2933.4987	5953.3540	0.0007	0.9997
GTR	43	-2930.7924	5954.9611	0.0003	1.0000
HKY	39	-2939.5756	5963.1861	0.0000	1.0000
K2PG	37	-2959.8751	5999.1683	0.0000	1.0000
K2PIG	38	-2959.8751	6001.4722	0.0000	1.0000
SYMG	41	-2958.6377	6005.9628	0.0000	1.0000
SYMIG	42	-2958.6373	6008.3018	0.0000	1.0000
K2PI	37	-2972.2642	6023.9465	0.0000	1.0000
SYMI	41	-2971.0102	6030.7077	0.0000	1.0000
K2P	36	-2979.4763	6036.0757	0.0000	1.0000
SYM	40	-2978.3866	6043.1298	0.0000	1.0000
F81G	39	-2987.8881	6059.8109	0.0000	1.0000
F81IG	40	-2988.5759	6063.5084	0.0000	1.0000
F81I	39	-2989.8743	6063.7833	0.0000	1.0000
F81	38	-2994.5697	6070.8614	0.0000	1.0000
JC69G	36	-3021.0835	6119.2900	0.0000	1.0000
JC69IG	37	-3021.0829	6121.5840	0.0000	1.0000
JC69I	36	-3023.7763	6124.6757	0.0000	1.0000
JC69	35	-3028.9925	6132.8219	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2921.9406	5931.8812	0.6673	0.6673
GTRIG	45	-2921.8830	5933.7661	0.2600	0.9274
GTRI	44	-2924.2249	5936.4498	0.0680	0.9954
HKYG	40	-2931.3753	5942.7506	0.0029	0.9983
HKYIG	41	-2931.3291	5944.6581	0.0011	0.9994
HKYI	40	-2933.4987	5946.9974	0.0003	0.9997
GTR	43	-2930.7924	5947.5849	0.0003	1.0000
HKY	39	-2939.5756	5957.1513	0.0000	1.0000
K2PG	37	-2959.8751	5993.7502	0.0000	1.0000
K2PIG	38	-2959.8751	5995.7502	0.0000	1.0000
SYMG	41	-2958.6377	5999.2754	0.0000	1.0000
SYMIG	42	-2958.6373	6001.2746	0.0000	1.0000
K2PI	37	-2972.2642	6018.5284	0.0000	1.0000
SYMI	41	-2971.0102	6024.0203	0.0000	1.0000
K2P	36	-2979.4763	6030.9526	0.0000	1.0000
SYM	40	-2978.3866	6036.7733	0.0000	1.0000
F81G	39	-2987.8881	6053.7761	0.0000	1.0000
F81IG	40	-2988.5759	6057.1518	0.0000	1.0000
F81I	39	-2989.8743	6057.7485	0.0000	1.0000
F81	38	-2994.5697	6065.1394	0.0000	1.0000
JC69G	36	-3021.0835	6114.1669	0.0000	1.0000
JC69IG	37	-3021.0829	6116.1659	0.0000	1.0000
JC69I	36	-3023.7763	6119.5526	0.0000	1.0000
JC69	35	-3028.9925	6127.9851	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2931.3753	6115.6532	0.8218	0.8218
HKYI	40	-2933.4987	6119.9000	0.0983	0.9201
HKYIG	41	-2931.3291	6121.8833	0.0365	0.9565
GTRG	44	-2921.9406	6122.0741	0.0331	0.9897
HKY	39	-2939.5756	6125.7313	0.0053	0.9950
GTRI	44	-2924.2249	6126.6427	0.0034	0.9984
GTRIG	45	-2921.8830	6128.2815	0.0015	0.9999
GTR	43	-2930.7924	6133.4552	0.0001	1.0000
K2PG	37	-2959.8751	6153.6851	0.0000	1.0000
K2PIG	38	-2959.8751	6160.0077	0.0000	1.0000
SYMG	41	-2958.6377	6176.5006	0.0000	1.0000
K2PI	37	-2972.2642	6178.4633	0.0000	1.0000
SYMIG	42	-2958.6373	6182.8223	0.0000	1.0000
K2P	36	-2979.4763	6186.5649	0.0000	1.0000
SYMI	41	-2971.0102	6201.2455	0.0000	1.0000
SYM	40	-2978.3866	6209.6759	0.0000	1.0000
F81G	39	-2987.8881	6222.3561	0.0000	1.0000
F81I	39	-2989.8743	6226.3286	0.0000	1.0000
F81	38	-2994.5697	6229.3969	0.0000	1.0000
F81IG	40	-2988.5759	6230.0544	0.0000	1.0000
JC69G	36	-3021.0835	6269.7793	0.0000	1.0000
JC69I	36	-3023.7763	6275.1650	0.0000	1.0000
JC69IG	37	-3021.0829	6276.1008	0.0000	1.0000
JC69	35	-3028.9925	6279.2748	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/chr4_7557.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7557.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7557.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7557.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 BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7557.phylip = 1 - 557;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7557.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

