
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:26 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_30195.phylip" (19 taxa, 510 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	-2003.8539	4104.2239	0.6499	0.6499
GTRIG	45	-2003.8539	4106.6303	0.1951	0.8450
GTRI	44	-2005.2944	4107.1050	0.1539	0.9989
HKYG	40	-2015.4746	4117.9427	0.0007	0.9996
HKYI	40	-2016.1527	4119.2990	0.0003	0.9999
HKYIG	41	-2016.2861	4121.9311	0.0001	1.0000
K2PG	37	-2032.6831	4145.3238	0.0000	1.0000
SYMG	41	-2028.6039	4146.5668	0.0000	1.0000
K2PI	37	-2033.4464	4146.8505	0.0000	1.0000
SYMIG	42	-2028.6037	4148.9419	0.0000	1.0000
K2PIG	38	-2034.1110	4150.5151	0.0000	1.0000
SYMI	41	-2031.0074	4151.3737	0.0000	1.0000
GTR	43	-2054.7300	4203.5802	0.0000	1.0000
HKY	39	-2066.7158	4218.0699	0.0000	1.0000
SYM	40	-2081.5791	4250.1519	0.0000	1.0000
K2P	36	-2086.9370	4251.5062	0.0000	1.0000
F81I	39	-2084.5272	4253.6927	0.0000	1.0000
F81G	39	-2084.5518	4253.7419	0.0000	1.0000
F81IG	40	-2084.5519	4256.0974	0.0000	1.0000
JC69G	36	-2097.4143	4272.4607	0.0000	1.0000
JC69I	36	-2097.5911	4272.8144	0.0000	1.0000
JC69IG	37	-2098.6623	4277.2822	0.0000	1.0000
F81	38	-2134.6052	4351.5034	0.0000	1.0000
JC69	35	-2148.5662	4372.4489	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-2003.8539	4095.7078	0.6229	0.6229
GTRIG	45	-2003.8539	4097.7079	0.2291	0.8520
GTRI	44	-2005.2944	4098.5889	0.1475	0.9995
HKYG	40	-2015.4746	4110.9491	0.0003	0.9998
HKYI	40	-2016.1527	4112.3054	0.0002	1.0000
HKYIG	41	-2016.2861	4114.5721	0.0000	1.0000
SYMG	41	-2028.6039	4139.2078	0.0000	1.0000
K2PG	37	-2032.6831	4139.3662	0.0000	1.0000
K2PI	37	-2033.4464	4140.8929	0.0000	1.0000
SYMIG	42	-2028.6037	4141.2074	0.0000	1.0000
SYMI	41	-2031.0074	4144.0148	0.0000	1.0000
K2PIG	38	-2034.1110	4144.2221	0.0000	1.0000
GTR	43	-2054.7300	4195.4600	0.0000	1.0000
HKY	39	-2066.7158	4211.4316	0.0000	1.0000
SYM	40	-2081.5791	4243.1583	0.0000	1.0000
K2P	36	-2086.9370	4245.8740	0.0000	1.0000
F81I	39	-2084.5272	4247.0544	0.0000	1.0000
F81G	39	-2084.5518	4247.1036	0.0000	1.0000
F81IG	40	-2084.5519	4249.1038	0.0000	1.0000
JC69G	36	-2097.4143	4266.8285	0.0000	1.0000
JC69I	36	-2097.5911	4267.1822	0.0000	1.0000
JC69IG	37	-2098.6623	4271.3246	0.0000	1.0000
F81	38	-2134.6052	4345.2104	0.0000	1.0000
JC69	35	-2148.5662	4367.1324	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-2015.4746	4280.3256	0.4816	0.4816
HKYI	40	-2016.1527	4281.6818	0.2444	0.7261
GTRG	44	-2003.8539	4282.0219	0.2062	0.9323
GTRI	44	-2005.2944	4284.9029	0.0488	0.9811
HKYIG	41	-2016.2861	4288.1830	0.0095	0.9906
GTRIG	45	-2003.8539	4288.2564	0.0091	0.9997
K2PG	37	-2032.6831	4296.0394	0.0002	0.9999
K2PI	37	-2033.4464	4297.5661	0.0001	1.0000
K2PIG	38	-2034.1110	4305.1297	0.0000	1.0000
SYMG	41	-2028.6039	4312.8186	0.0000	1.0000
SYMI	41	-2031.0074	4317.6256	0.0000	1.0000
SYMIG	42	-2028.6037	4319.0527	0.0000	1.0000
HKY	39	-2066.7158	4376.5736	0.0000	1.0000
GTR	43	-2054.7300	4377.5397	0.0000	1.0000
K2P	36	-2086.9370	4398.3128	0.0000	1.0000
F81I	39	-2084.5272	4412.1965	0.0000	1.0000
F81G	39	-2084.5518	4412.2457	0.0000	1.0000
SYM	40	-2081.5791	4412.5347	0.0000	1.0000
F81IG	40	-2084.5519	4418.4802	0.0000	1.0000
JC69G	36	-2097.4143	4419.2673	0.0000	1.0000
JC69I	36	-2097.5911	4419.6210	0.0000	1.0000
JC69IG	37	-2098.6623	4427.9978	0.0000	1.0000
F81	38	-2134.6052	4506.1180	0.0000	1.0000
JC69	35	-2148.5662	4515.3368	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_30195.phylip = 1 - 510;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30195.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_30195.phylip = 1 - 510;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30195.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/chr1_30195.phylip = 1 - 510;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_30195.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

