
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:13 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/chr1_28784.phylip" (19 taxa, 521 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: GTRG


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	-1960.0390	4016.3973	0.5823	0.5823
GTRIG	45	-1959.8474	4018.4107	0.2128	0.7951
GTRI	44	-1961.0846	4018.4885	0.2047	0.9998
HKYG	40	-1973.2662	4033.3658	0.0001	0.9999
HKYI	40	-1973.8176	4034.4685	0.0001	1.0000
HKYIG	41	-1973.0345	4035.2590	0.0000	1.0000
GTR	43	-1980.5341	4055.0012	0.0000	1.0000
SYMG	41	-1983.0125	4055.2150	0.0000	1.0000
SYMI	41	-1983.6270	4056.4440	0.0000	1.0000
K2PG	37	-1988.6441	4057.1101	0.0000	1.0000
SYMIG	42	-1982.8127	4057.1818	0.0000	1.0000
K2PI	37	-1989.2779	4058.3777	0.0000	1.0000
K2PIG	38	-1988.4639	4059.0771	0.0000	1.0000
HKY	39	-1992.1665	4068.8195	0.0000	1.0000
SYM	40	-2001.3136	4089.4604	0.0000	1.0000
K2P	36	-2007.4369	4092.3780	0.0000	1.0000
F81G	39	-2033.6140	4151.7145	0.0000	1.0000
F81I	39	-2034.0122	4152.5109	0.0000	1.0000
F81IG	40	-2033.3752	4153.5837	0.0000	1.0000
JC69G	36	-2043.7135	4164.9312	0.0000	1.0000
JC69I	36	-2044.1554	4165.8149	0.0000	1.0000
JC69IG	37	-2043.4997	4166.8214	0.0000	1.0000
F81	38	-2050.9966	4184.1426	0.0000	1.0000
JC69	35	-2061.1785	4197.5529	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1960.0390	4008.0779	0.5564	0.5564
GTRIG	45	-1959.8474	4009.6949	0.2479	0.8043
GTRI	44	-1961.0846	4010.1692	0.1956	0.9999
HKYG	40	-1973.2662	4026.5324	0.0001	0.9999
HKYI	40	-1973.8176	4027.6351	0.0000	1.0000
HKYIG	41	-1973.0345	4028.0691	0.0000	1.0000
GTR	43	-1980.5341	4047.0683	0.0000	1.0000
SYMG	41	-1983.0125	4048.0250	0.0000	1.0000
SYMI	41	-1983.6270	4049.2540	0.0000	1.0000
SYMIG	42	-1982.8127	4049.6253	0.0000	1.0000
K2PG	37	-1988.6441	4051.2881	0.0000	1.0000
K2PI	37	-1989.2779	4052.5558	0.0000	1.0000
K2PIG	38	-1988.4639	4052.9277	0.0000	1.0000
HKY	39	-1992.1665	4062.3330	0.0000	1.0000
SYM	40	-2001.3136	4082.6271	0.0000	1.0000
K2P	36	-2007.4369	4086.8738	0.0000	1.0000
F81G	39	-2033.6140	4145.2280	0.0000	1.0000
F81I	39	-2034.0122	4146.0244	0.0000	1.0000
F81IG	40	-2033.3752	4146.7504	0.0000	1.0000
JC69G	36	-2043.7135	4159.4271	0.0000	1.0000
JC69I	36	-2044.1554	4160.3107	0.0000	1.0000
JC69IG	37	-2043.4997	4160.9994	0.0000	1.0000
F81	38	-2050.9966	4177.9932	0.0000	1.0000
JC69	35	-2061.1785	4192.3570	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1960.0390	4195.3309	0.4537	0.4537
HKYG	40	-1973.2662	4196.7624	0.2218	0.6755
GTRI	44	-1961.0846	4197.4222	0.1595	0.8350
HKYI	40	-1973.8176	4197.8651	0.1278	0.9628
GTRIG	45	-1959.8474	4201.2037	0.0241	0.9869
HKYIG	41	-1973.0345	4202.5548	0.0123	0.9991
K2PG	37	-1988.6441	4208.7509	0.0006	0.9997
K2PI	37	-1989.2779	4210.0185	0.0003	1.0000
K2PIG	38	-1988.4639	4214.6462	0.0000	1.0000
SYMG	41	-1983.0125	4222.5108	0.0000	1.0000
SYMI	41	-1983.6270	4223.7398	0.0000	1.0000
HKY	39	-1992.1665	4228.3073	0.0000	1.0000
SYMIG	42	-1982.8127	4228.3668	0.0000	1.0000
GTR	43	-1980.5341	4230.0655	0.0000	1.0000
K2P	36	-2007.4369	4240.0808	0.0000	1.0000
SYM	40	-2001.3136	4252.8571	0.0000	1.0000
F81G	39	-2033.6140	4311.2023	0.0000	1.0000
F81I	39	-2034.0122	4311.9987	0.0000	1.0000
JC69G	36	-2043.7135	4312.6341	0.0000	1.0000
JC69I	36	-2044.1554	4313.5177	0.0000	1.0000
F81IG	40	-2033.3752	4316.9804	0.0000	1.0000
JC69IG	37	-2043.4997	4318.4622	0.0000	1.0000
F81	38	-2050.9966	4339.7117	0.0000	1.0000
JC69	35	-2061.1785	4341.3083	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/chr1_28784.phylip = 1 - 521;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28784.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/chr1_28784.phylip = 1 - 521;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28784.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28784.phylip = 1 - 521;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_28784.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;


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End of Output

