
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:21 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/chr17_2963.phylip" (19 taxa, 724 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	-2019.6919	4133.2159	0.5821	0.5821
GTRIG	45	-2019.5678	4135.2417	0.2114	0.7935
GTRI	44	-2021.0177	4135.8674	0.1546	0.9481
HKYG	40	-2027.1000	4139.0024	0.0322	0.9804
HKYIG	41	-2027.0533	4141.1565	0.0110	0.9914
HKYI	40	-2028.4196	4141.6416	0.0086	1.0000
K2PG	37	-2040.9174	4159.9339	0.0000	1.0000
K2PI	37	-2041.6807	4161.4606	0.0000	1.0000
SYMG	41	-2038.0401	4163.1300	0.0000	1.0000
K2PIG	38	-2041.5544	4163.4357	0.0000	1.0000
SYMIG	42	-2037.8222	4164.9483	0.0000	1.0000
SYMI	41	-2039.0361	4165.1221	0.0000	1.0000
GTR	43	-2040.2108	4171.9864	0.0000	1.0000
HKY	39	-2046.3986	4175.3587	0.0000	1.0000
K2P	36	-2060.8234	4197.5246	0.0000	1.0000
SYM	40	-2058.4761	4201.7546	0.0000	1.0000
F81G	39	-2081.7917	4246.1448	0.0000	1.0000
F81IG	40	-2081.6575	4248.1174	0.0000	1.0000
F81I	39	-2082.8585	4248.2783	0.0000	1.0000
JC69G	36	-2093.3961	4262.6699	0.0000	1.0000
JC69IG	37	-2093.2450	4264.5891	0.0000	1.0000
JC69I	36	-2094.4418	4264.7612	0.0000	1.0000
F81	38	-2100.5502	4281.4274	0.0000	1.0000
JC69	35	-2108.1139	4289.8905	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2019.6919	4127.3838	0.5758	0.5758
GTRIG	45	-2019.5678	4129.1355	0.2398	0.8156
GTRI	44	-2021.0177	4130.0353	0.1529	0.9685
HKYG	40	-2027.1000	4134.2000	0.0191	0.9876
HKYIG	41	-2027.0533	4136.1066	0.0073	0.9949
HKYI	40	-2028.4196	4136.8393	0.0051	1.0000
K2PG	37	-2040.9174	4155.8348	0.0000	1.0000
K2PI	37	-2041.6807	4157.3615	0.0000	1.0000
SYMG	41	-2038.0401	4158.0802	0.0000	1.0000
K2PIG	38	-2041.5544	4159.1087	0.0000	1.0000
SYMIG	42	-2037.8222	4159.6444	0.0000	1.0000
SYMI	41	-2039.0361	4160.0723	0.0000	1.0000
GTR	43	-2040.2108	4166.4217	0.0000	1.0000
HKY	39	-2046.3986	4170.7973	0.0000	1.0000
K2P	36	-2060.8234	4193.6469	0.0000	1.0000
SYM	40	-2058.4761	4196.9522	0.0000	1.0000
F81G	39	-2081.7917	4241.5834	0.0000	1.0000
F81IG	40	-2081.6575	4243.3151	0.0000	1.0000
F81I	39	-2082.8585	4243.7169	0.0000	1.0000
JC69G	36	-2093.3961	4258.7922	0.0000	1.0000
JC69IG	37	-2093.2450	4260.4900	0.0000	1.0000
JC69I	36	-2094.4418	4260.8835	0.0000	1.0000
F81	38	-2100.5502	4277.1004	0.0000	1.0000
JC69	35	-2108.1139	4286.2277	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2027.1000	4317.5917	0.7467	0.7467
HKYI	40	-2028.4196	4320.2309	0.1996	0.9463
HKYIG	41	-2027.0533	4324.0831	0.0291	0.9754
K2PG	37	-2040.9174	4325.4721	0.0145	0.9899
K2PI	37	-2041.6807	4326.9988	0.0068	0.9966
GTRG	44	-2019.6919	4329.1146	0.0023	0.9990
GTRI	44	-2021.0177	4331.7662	0.0006	0.9996
K2PIG	38	-2041.5544	4333.3308	0.0003	0.9999
GTRIG	45	-2019.5678	4335.4512	0.0001	1.0000
SYMG	41	-2038.0401	4346.0566	0.0000	1.0000
SYMI	41	-2039.0361	4348.0487	0.0000	1.0000
HKY	39	-2046.3986	4349.6041	0.0000	1.0000
SYMIG	42	-2037.8222	4352.2056	0.0000	1.0000
K2P	36	-2060.8234	4358.6994	0.0000	1.0000
GTR	43	-2040.2108	4363.5677	0.0000	1.0000
SYM	40	-2058.4761	4380.3439	0.0000	1.0000
F81G	39	-2081.7917	4420.3902	0.0000	1.0000
F81I	39	-2082.8585	4422.5238	0.0000	1.0000
JC69G	36	-2093.3961	4423.8447	0.0000	1.0000
JC69I	36	-2094.4418	4425.9360	0.0000	1.0000
F81IG	40	-2081.6575	4426.7068	0.0000	1.0000
JC69IG	37	-2093.2450	4430.1272	0.0000	1.0000
JC69	35	-2108.1139	4446.6954	0.0000	1.0000
F81	38	-2100.5502	4451.3225	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/chr17_2963.phylip = 1 - 724;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2963.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/chr17_2963.phylip = 1 - 724;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2963.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/chr17_2963.phylip = 1 - 724;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2963.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

