
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:11 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/chr8_4067.phylip" (19 taxa, 667 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	-2016.8910	4119.0215	0.5112	0.5112
HKYIG	41	-2016.7089	4120.9281	0.1970	0.7082
GTRG	44	-2013.6122	4121.5909	0.1415	0.8497
GTRIG	45	-2013.2324	4123.1315	0.0655	0.9152
HKYI	40	-2019.2896	4123.8189	0.0464	0.9616
GTRI	44	-2014.9176	4124.2018	0.0383	1.0000
K2PG	37	-2030.1706	4138.8117	0.0000	1.0000
K2PIG	38	-2030.0625	4140.8448	0.0000	1.0000
K2PI	37	-2031.6373	4141.7451	0.0000	1.0000
SYMG	41	-2027.9324	4143.3752	0.0000	1.0000
SYMIG	42	-2027.8187	4145.4258	0.0000	1.0000
SYMI	41	-2029.3603	4146.2310	0.0000	1.0000
HKY	39	-2038.7024	4160.3808	0.0000	1.0000
GTR	43	-2035.1427	4162.3593	0.0000	1.0000
F81G	39	-2043.7984	4170.5729	0.0000	1.0000
F81IG	40	-2043.6653	4172.5702	0.0000	1.0000
K2P	36	-2050.0732	4176.3749	0.0000	1.0000
F81I	39	-2046.8820	4176.7402	0.0000	1.0000
SYM	40	-2047.9834	4181.2063	0.0000	1.0000
JC69G	36	-2053.7026	4183.6339	0.0000	1.0000
JC69IG	37	-2053.5930	4185.6566	0.0000	1.0000
JC69I	36	-2056.9662	4190.1611	0.0000	1.0000
F81	38	-2065.1417	4211.0030	0.0000	1.0000
JC69	35	-2074.6768	4223.3472	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-2016.8910	4113.7819	0.4147	0.4147
GTRG	44	-2013.6122	4115.2244	0.2016	0.6162
HKYIG	41	-2016.7089	4115.4177	0.1830	0.7992
GTRIG	45	-2013.2324	4116.4648	0.1084	0.9077
GTRI	44	-2014.9176	4117.8352	0.0546	0.9623
HKYI	40	-2019.2896	4118.5793	0.0377	1.0000
K2PG	37	-2030.1706	4134.3412	0.0000	1.0000
K2PIG	38	-2030.0625	4136.1251	0.0000	1.0000
K2PI	37	-2031.6373	4137.2745	0.0000	1.0000
SYMG	41	-2027.9324	4137.8648	0.0000	1.0000
SYMIG	42	-2027.8187	4139.6374	0.0000	1.0000
SYMI	41	-2029.3603	4140.7206	0.0000	1.0000
HKY	39	-2038.7024	4155.4047	0.0000	1.0000
GTR	43	-2035.1427	4156.2854	0.0000	1.0000
F81G	39	-2043.7984	4165.5968	0.0000	1.0000
F81IG	40	-2043.6653	4167.3306	0.0000	1.0000
F81I	39	-2046.8820	4171.7641	0.0000	1.0000
K2P	36	-2050.0732	4172.1464	0.0000	1.0000
SYM	40	-2047.9834	4175.9667	0.0000	1.0000
JC69G	36	-2053.7026	4179.4053	0.0000	1.0000
JC69IG	37	-2053.5930	4181.1861	0.0000	1.0000
JC69I	36	-2056.9662	4185.9325	0.0000	1.0000
F81	38	-2065.1417	4206.2833	0.0000	1.0000
JC69	35	-2074.6768	4219.3535	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2016.8910	4293.8935	0.8512	0.8512
HKYI	40	-2019.2896	4298.6909	0.0773	0.9285
HKYIG	41	-2016.7089	4300.0321	0.0395	0.9680
K2PG	37	-2030.1706	4300.9444	0.0251	0.9931
K2PI	37	-2031.6373	4303.8778	0.0058	0.9989
K2PIG	38	-2030.0625	4307.2311	0.0011	0.9999
GTRG	44	-2013.6122	4313.3471	0.0001	1.0000
GTRI	44	-2014.9176	4315.9580	0.0000	1.0000
GTRIG	45	-2013.2324	4319.0904	0.0000	1.0000
SYMG	41	-2027.9324	4322.4792	0.0000	1.0000
SYMI	41	-2029.3603	4325.3350	0.0000	1.0000
SYMIG	42	-2027.8187	4328.7545	0.0000	1.0000
HKY	39	-2038.7024	4331.0135	0.0000	1.0000
K2P	36	-2050.0732	4334.2468	0.0000	1.0000
F81G	39	-2043.7984	4341.2056	0.0000	1.0000
JC69G	36	-2053.7026	4341.5057	0.0000	1.0000
F81I	39	-2046.8820	4347.3729	0.0000	1.0000
F81IG	40	-2043.6653	4347.4422	0.0000	1.0000
JC69IG	37	-2053.5930	4347.7893	0.0000	1.0000
JC69I	36	-2056.9662	4348.0329	0.0000	1.0000
GTR	43	-2035.1427	4349.9054	0.0000	1.0000
SYM	40	-2047.9834	4356.0783	0.0000	1.0000
JC69	35	-2074.6768	4376.9512	0.0000	1.0000
F81	38	-2065.1417	4377.3893	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/chr8_4067.phylip = 1 - 667;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4067.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/chr8_4067.phylip = 1 - 667;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4067.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/chr8_4067.phylip = 1 - 667;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4067.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

