
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:53 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/chr7_6366.phylip" (19 taxa, 634 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	-1960.5623	4015.8478	0.5589	0.5589
GTRIG	45	-1960.0992	4017.2392	0.2787	0.8376
GTRI	44	-1961.8681	4018.4594	0.1514	0.9890
HKYG	40	-1969.9928	4025.5168	0.0044	0.9934
HKYI	40	-1970.1227	4025.7765	0.0039	0.9973
HKYIG	41	-1969.9373	4027.6923	0.0015	0.9988
SYMG	41	-1970.8133	4029.4441	0.0006	0.9995
SYMI	41	-1971.6351	4031.0877	0.0003	0.9997
SYMIG	42	-1970.6024	4031.3165	0.0002	1.0000
K2PG	37	-1979.8276	4038.3734	0.0000	1.0000
K2PI	37	-1980.0643	4038.8468	0.0000	1.0000
K2PIG	38	-1979.8283	4040.6381	0.0000	1.0000
GTR	43	-2002.7412	4097.8960	0.0000	1.0000
HKY	39	-2011.3980	4106.0485	0.0000	1.0000
SYM	40	-2011.5428	4108.6169	0.0000	1.0000
K2P	36	-2020.7633	4117.9890	0.0000	1.0000
F81I	39	-2017.9344	4119.1214	0.0000	1.0000
F81G	39	-2018.1257	4119.5039	0.0000	1.0000
F81IG	40	-2018.8682	4123.2675	0.0000	1.0000
JC69I	36	-2025.6452	4127.7527	0.0000	1.0000
JC69G	36	-2025.9952	4128.4526	0.0000	1.0000
JC69IG	37	-2025.9951	4130.7084	0.0000	1.0000
F81	38	-2054.5790	4190.1396	0.0000	1.0000
JC69	35	-2062.0225	4198.2591	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1960.5623	4009.1246	0.5357	0.5357
GTRIG	45	-1960.0992	4010.1984	0.3131	0.8488
GTRI	44	-1961.8681	4011.7361	0.1451	0.9940
HKYG	40	-1969.9928	4019.9856	0.0023	0.9963
HKYI	40	-1970.1227	4020.2453	0.0021	0.9984
HKYIG	41	-1969.9373	4021.8747	0.0009	0.9993
SYMG	41	-1970.8133	4023.6266	0.0004	0.9997
SYMIG	42	-1970.6024	4025.2049	0.0002	0.9998
SYMI	41	-1971.6351	4025.2702	0.0002	1.0000
K2PG	37	-1979.8276	4033.6553	0.0000	1.0000
K2PI	37	-1980.0643	4034.1286	0.0000	1.0000
K2PIG	38	-1979.8283	4035.6566	0.0000	1.0000
GTR	43	-2002.7412	4091.4825	0.0000	1.0000
HKY	39	-2011.3980	4100.7960	0.0000	1.0000
SYM	40	-2011.5428	4103.0857	0.0000	1.0000
K2P	36	-2020.7633	4113.5266	0.0000	1.0000
F81I	39	-2017.9344	4113.8688	0.0000	1.0000
F81G	39	-2018.1257	4114.2514	0.0000	1.0000
F81IG	40	-2018.8682	4117.7363	0.0000	1.0000
JC69I	36	-2025.6452	4123.2904	0.0000	1.0000
JC69G	36	-2025.9952	4123.9903	0.0000	1.0000
JC69IG	37	-2025.9951	4125.9903	0.0000	1.0000
F81	38	-2054.5790	4185.1581	0.0000	1.0000
JC69	35	-2062.0225	4194.0450	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1969.9928	4198.0675	0.2816	0.2816
HKYI	40	-1970.1227	4198.3273	0.2473	0.5289
K2PG	37	-1979.8276	4198.3811	0.2407	0.7696
K2PI	37	-1980.0643	4198.8545	0.1900	0.9596
HKYIG	41	-1969.9373	4204.4087	0.0118	0.9715
K2PIG	38	-1979.8283	4204.8345	0.0096	0.9810
GTRG	44	-1960.5623	4205.0147	0.0087	0.9898
SYMG	41	-1970.8133	4206.1606	0.0049	0.9947
GTRI	44	-1961.8681	4207.6263	0.0024	0.9970
SYMI	41	-1971.6351	4207.8042	0.0022	0.9992
GTRIG	45	-1960.0992	4210.5406	0.0006	0.9998
SYMIG	42	-1970.6024	4212.1909	0.0002	1.0000
K2P	36	-2020.7633	4273.8004	0.0000	1.0000
HKY	39	-2011.3980	4274.4259	0.0000	1.0000
SYM	40	-2011.5428	4281.1676	0.0000	1.0000
GTR	43	-2002.7412	4282.9206	0.0000	1.0000
JC69I	36	-2025.6452	4283.5641	0.0000	1.0000
JC69G	36	-2025.9952	4284.2641	0.0000	1.0000
F81I	39	-2017.9344	4287.4987	0.0000	1.0000
F81G	39	-2018.1257	4287.8813	0.0000	1.0000
JC69IG	37	-2025.9951	4290.7161	0.0000	1.0000
F81IG	40	-2018.8682	4295.8183	0.0000	1.0000
JC69	35	-2062.0225	4349.8667	0.0000	1.0000
F81	38	-2054.5790	4354.3359	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/chr7_6366.phylip = 1 - 634;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6366.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/chr7_6366.phylip = 1 - 634;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6366.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/chr7_6366.phylip = 1 - 634;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_6366.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;


-------------------------------------------------------------
End of Output

