
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:57 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/chr6_5974.phylip" (19 taxa, 790 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-1976.8161	4038.0114	0.3937	0.3937
HKYIG	41	-1976.2695	4039.1433	0.2236	0.6173
HKYI	40	-1977.4334	4039.2459	0.2124	0.8297
GTRG	44	-1973.9164	4041.1482	0.0820	0.9117
GTRIG	45	-1973.3868	4042.3382	0.0453	0.9570
GTRI	44	-1974.5628	4042.4410	0.0430	1.0000
K2PG	37	-1991.3350	4060.4094	0.0000	1.0000
K2PIG	38	-1990.7663	4061.4794	0.0000	1.0000
K2PI	37	-1991.9661	4061.6715	0.0000	1.0000
SYMG	41	-1990.2902	4067.1847	0.0000	1.0000
SYMIG	42	-1989.7452	4068.3258	0.0000	1.0000
SYMI	41	-1990.9393	4068.4828	0.0000	1.0000
HKY	39	-1997.4570	4077.0740	0.0000	1.0000
GTR	43	-1994.2661	4079.6045	0.0000	1.0000
K2P	36	-2012.3755	4100.2888	0.0000	1.0000
F81G	39	-2010.2523	4102.6646	0.0000	1.0000
F81IG	40	-2009.5734	4103.5259	0.0000	1.0000
F81I	39	-2011.1493	4104.4586	0.0000	1.0000
SYM	40	-2010.8567	4106.0927	0.0000	1.0000
JC69G	36	-2023.2861	4122.1101	0.0000	1.0000
JC69IG	37	-2022.5849	4122.9091	0.0000	1.0000
JC69I	36	-2024.1649	4123.8676	0.0000	1.0000
F81	38	-2030.2830	4140.5128	0.0000	1.0000
JC69	35	-2043.5621	4160.4663	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1976.8161	4033.6322	0.3460	0.3460
HKYIG	41	-1976.2695	4034.5391	0.2199	0.5659
HKYI	40	-1977.4334	4034.8667	0.1867	0.7526
GTRG	44	-1973.9164	4035.8327	0.1152	0.8677
GTRIG	45	-1973.3868	4036.7737	0.0719	0.9397
GTRI	44	-1974.5628	4037.1256	0.0603	1.0000
K2PG	37	-1991.3350	4056.6701	0.0000	1.0000
K2PIG	38	-1990.7663	4057.5327	0.0000	1.0000
K2PI	37	-1991.9661	4057.9321	0.0000	1.0000
SYMG	41	-1990.2902	4062.5804	0.0000	1.0000
SYMIG	42	-1989.7452	4063.4905	0.0000	1.0000
SYMI	41	-1990.9393	4063.8786	0.0000	1.0000
HKY	39	-1997.4570	4072.9140	0.0000	1.0000
GTR	43	-1994.2661	4074.5321	0.0000	1.0000
K2P	36	-2012.3755	4096.7510	0.0000	1.0000
F81G	39	-2010.2523	4098.5046	0.0000	1.0000
F81IG	40	-2009.5734	4099.1467	0.0000	1.0000
F81I	39	-2011.1493	4100.2986	0.0000	1.0000
SYM	40	-2010.8567	4101.7135	0.0000	1.0000
JC69G	36	-2023.2861	4118.5722	0.0000	1.0000
JC69IG	37	-2022.5849	4119.1698	0.0000	1.0000
JC69I	36	-2024.1649	4120.3297	0.0000	1.0000
F81	38	-2030.2830	4136.5660	0.0000	1.0000
JC69	35	-2043.5621	4157.1242	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1976.8161	4220.5136	0.6179	0.6179
HKYI	40	-1977.4334	4221.7480	0.3333	0.9512
HKYIG	41	-1976.2695	4226.0924	0.0380	0.9891
K2PG	37	-1991.3350	4229.5353	0.0068	0.9959
K2PI	37	-1991.9661	4230.7973	0.0036	0.9995
K2PIG	38	-1990.7663	4235.0699	0.0004	1.0000
GTRG	44	-1973.9164	4241.4022	0.0000	1.0000
GTRI	44	-1974.5628	4242.6950	0.0000	1.0000
GTRIG	45	-1973.3868	4247.0152	0.0000	1.0000
SYMG	41	-1990.2902	4254.1338	0.0000	1.0000
HKY	39	-1997.4570	4255.1232	0.0000	1.0000
SYMI	41	-1990.9393	4255.4319	0.0000	1.0000
SYMIG	42	-1989.7452	4259.7158	0.0000	1.0000
K2P	36	-2012.3755	4264.9441	0.0000	1.0000
GTR	43	-1994.2661	4275.4295	0.0000	1.0000
F81G	39	-2010.2523	4280.7139	0.0000	1.0000
F81I	39	-2011.1493	4282.5079	0.0000	1.0000
F81IG	40	-2009.5734	4286.0281	0.0000	1.0000
JC69G	36	-2023.2861	4286.7654	0.0000	1.0000
JC69I	36	-2024.1649	4288.5229	0.0000	1.0000
SYM	40	-2010.8567	4288.5948	0.0000	1.0000
JC69IG	37	-2022.5849	4292.0350	0.0000	1.0000
F81	38	-2030.2830	4314.1033	0.0000	1.0000
JC69	35	-2043.5621	4320.6453	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_5974.phylip = 1 - 790;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_5974.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_5974.phylip = 1 - 790;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_5974.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;


[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/chr6_5974.phylip = 1 - 790;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_5974.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

