
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:11 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/chr3_5776.phylip" (19 taxa, 518 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	-1964.8629	4026.0979	0.4084	0.4084
HKYG	40	-1969.9961	4026.8686	0.2778	0.6862
GTRIG	45	-1964.5140	4027.7991	0.1745	0.8607
HKYIG	41	-1969.5560	4028.3473	0.1326	0.9933
GTRI	44	-1969.6666	4035.7053	0.0033	0.9966
HKYI	40	-1974.4363	4035.7490	0.0033	0.9999
K2PG	37	-1982.5848	4045.0279	0.0000	1.0000
SYMG	41	-1978.2934	4045.8222	0.0000	1.0000
K2PIG	38	-1982.0386	4046.2650	0.0000	1.0000
SYMIG	42	-1977.7884	4047.1810	0.0000	1.0000
K2PI	37	-1986.7701	4053.3986	0.0000	1.0000
SYMI	41	-1983.7107	4056.6566	0.0000	1.0000
F81G	39	-2017.0002	4118.5276	0.0000	1.0000
F81IG	40	-2016.7227	4120.3218	0.0000	1.0000
F81I	39	-2019.8649	4124.2570	0.0000	1.0000
JC69G	36	-2026.4915	4130.5215	0.0000	1.0000
JC69IG	37	-2026.1241	4132.1065	0.0000	1.0000
JC69I	36	-2029.5683	4136.6751	0.0000	1.0000
GTR	43	-2033.8054	4161.5939	0.0000	1.0000
HKY	39	-2039.4005	4163.3282	0.0000	1.0000
K2P	36	-2050.1229	4177.7842	0.0000	1.0000
SYM	40	-2045.8213	4178.5190	0.0000	1.0000
F81	38	-2079.9137	4242.0153	0.0000	1.0000
JC69	35	-2089.3985	4254.0251	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1964.8629	4017.7258	0.4903	0.4903
GTRIG	45	-1964.5140	4019.0279	0.2557	0.7460
HKYG	40	-1969.9961	4019.9923	0.1579	0.9039
HKYIG	41	-1969.5560	4021.1120	0.0902	0.9941
GTRI	44	-1969.6666	4027.3332	0.0040	0.9981
HKYI	40	-1974.4363	4028.8727	0.0019	1.0000
SYMG	41	-1978.2934	4038.5869	0.0000	1.0000
K2PG	37	-1982.5848	4039.1696	0.0000	1.0000
SYMIG	42	-1977.7884	4039.5768	0.0000	1.0000
K2PIG	38	-1982.0386	4040.0771	0.0000	1.0000
K2PI	37	-1986.7701	4047.5403	0.0000	1.0000
SYMI	41	-1983.7107	4049.4213	0.0000	1.0000
F81G	39	-2017.0002	4112.0004	0.0000	1.0000
F81IG	40	-2016.7227	4113.4455	0.0000	1.0000
F81I	39	-2019.8649	4117.7298	0.0000	1.0000
JC69G	36	-2026.4915	4124.9830	0.0000	1.0000
JC69IG	37	-2026.1241	4126.2482	0.0000	1.0000
JC69I	36	-2029.5683	4131.1366	0.0000	1.0000
GTR	43	-2033.8054	4153.6108	0.0000	1.0000
HKY	39	-2039.4005	4156.8010	0.0000	1.0000
SYM	40	-2045.8213	4171.6427	0.0000	1.0000
K2P	36	-2050.1229	4172.2458	0.0000	1.0000
F81	38	-2079.9137	4235.8274	0.0000	1.0000
JC69	35	-2089.3985	4248.7969	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1969.9961	4189.9913	0.8892	0.8892
HKYIG	41	-1969.5560	4195.3609	0.0607	0.9499
K2PG	37	-1982.5848	4196.4187	0.0358	0.9856
HKYI	40	-1974.4363	4198.8717	0.0105	0.9961
K2PIG	38	-1982.0386	4201.5762	0.0027	0.9988
GTRG	44	-1964.8629	4204.7247	0.0006	0.9994
K2PI	37	-1986.7701	4204.7893	0.0005	0.9999
GTRIG	45	-1964.5140	4210.2768	0.0000	1.0000
SYMG	41	-1978.2934	4212.8358	0.0000	1.0000
GTRI	44	-1969.6666	4214.3321	0.0000	1.0000
SYMIG	42	-1977.7884	4218.0757	0.0000	1.0000
SYMI	41	-1983.7107	4223.6703	0.0000	1.0000
F81G	39	-2017.0002	4277.7494	0.0000	1.0000
JC69G	36	-2026.4915	4277.9821	0.0000	1.0000
F81IG	40	-2016.7227	4283.4445	0.0000	1.0000
F81I	39	-2019.8649	4283.4788	0.0000	1.0000
JC69IG	37	-2026.1241	4283.4972	0.0000	1.0000
JC69I	36	-2029.5683	4284.1357	0.0000	1.0000
HKY	39	-2039.4005	4322.5501	0.0000	1.0000
K2P	36	-2050.1229	4325.2449	0.0000	1.0000
GTR	43	-2033.8054	4336.3598	0.0000	1.0000
SYM	40	-2045.8213	4341.6417	0.0000	1.0000
F81	38	-2079.9137	4397.3264	0.0000	1.0000
JC69	35	-2089.3985	4397.5461	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/chr3_5776.phylip = 1 - 518;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5776.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/chr3_5776.phylip = 1 - 518;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5776.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/chr3_5776.phylip = 1 - 518;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_5776.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

