
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:58 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/chr7_2669.phylip" (19 taxa, 1014 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	-3356.0333	6804.1532	0.5871	0.5871
GTRIG	45	-3355.2916	6804.8600	0.4123	0.9994
GTRI	44	-3363.1299	6818.3466	0.0005	0.9999
HKYG	40	-3369.5583	6822.4876	0.0001	0.9999
HKYIG	41	-3368.6064	6822.7560	0.0001	1.0000
HKYI	40	-3375.8538	6835.0787	0.0000	1.0000
K2PIG	38	-3404.8130	6888.6660	0.0000	1.0000
K2PG	37	-3405.8956	6888.6724	0.0000	1.0000
SYMG	41	-3402.0069	6889.5569	0.0000	1.0000
SYMIG	42	-3401.0801	6889.8802	0.0000	1.0000
K2PI	37	-3411.8428	6900.5668	0.0000	1.0000
SYMI	41	-3407.9864	6901.5160	0.0000	1.0000
GTR	43	-3407.1019	6904.1048	0.0000	1.0000
HKY	39	-3420.3830	6921.9694	0.0000	1.0000
F81G	39	-3451.6854	6984.5742	0.0000	1.0000
F81IG	40	-3450.9149	6985.2007	0.0000	1.0000
SYM	40	-3452.6313	6988.6336	0.0000	1.0000
K2P	36	-3458.1582	6991.0432	0.0000	1.0000
F81I	39	-3457.1009	6995.4050	0.0000	1.0000
JC69G	36	-3480.8179	7036.3624	0.0000	1.0000
JC69IG	37	-3479.9580	7036.7972	0.0000	1.0000
JC69I	36	-3486.2421	7047.2109	0.0000	1.0000
F81	38	-3499.2958	7077.6315	0.0000	1.0000
JC69	35	-3529.7762	7132.1291	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-3356.0333	6800.0665	0.5639	0.5639
GTRIG	45	-3355.2916	6800.5832	0.4355	0.9995
GTRI	44	-3363.1299	6814.2599	0.0005	0.9999
HKYG	40	-3369.5583	6819.1165	0.0000	1.0000
HKYIG	41	-3368.6064	6819.2128	0.0000	1.0000
HKYI	40	-3375.8538	6831.7077	0.0000	1.0000
K2PIG	38	-3404.8130	6885.6260	0.0000	1.0000
K2PG	37	-3405.8956	6885.7913	0.0000	1.0000
SYMG	41	-3402.0069	6886.0137	0.0000	1.0000
SYMIG	42	-3401.0801	6886.1603	0.0000	1.0000
K2PI	37	-3411.8428	6897.6857	0.0000	1.0000
SYMI	41	-3407.9864	6897.9728	0.0000	1.0000
GTR	43	-3407.1019	6900.2037	0.0000	1.0000
HKY	39	-3420.3830	6918.7661	0.0000	1.0000
F81G	39	-3451.6854	6981.3709	0.0000	1.0000
F81IG	40	-3450.9149	6981.8297	0.0000	1.0000
SYM	40	-3452.6313	6985.2626	0.0000	1.0000
K2P	36	-3458.1582	6988.3164	0.0000	1.0000
F81I	39	-3457.1009	6992.2017	0.0000	1.0000
JC69G	36	-3480.8179	7033.6357	0.0000	1.0000
JC69IG	37	-3479.9580	7033.9161	0.0000	1.0000
JC69I	36	-3486.2421	7044.4842	0.0000	1.0000
F81	38	-3499.2958	7074.5915	0.0000	1.0000
JC69	35	-3529.7762	7129.5524	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3369.5583	7015.9829	0.5379	0.5379
GTRG	44	-3356.0333	7016.6195	0.3912	0.9291
HKYIG	41	-3368.6064	7021.0008	0.0438	0.9729
GTRIG	45	-3355.2916	7022.0578	0.0258	0.9987
HKYI	40	-3375.8538	7028.5740	0.0010	0.9997
GTRI	44	-3363.1299	7030.8128	0.0003	1.0000
K2PG	37	-3405.8956	7067.8927	0.0000	1.0000
K2PIG	38	-3404.8130	7072.6490	0.0000	1.0000
K2PI	37	-3411.8428	7079.7870	0.0000	1.0000
SYMG	41	-3402.0069	7087.8017	0.0000	1.0000
SYMIG	42	-3401.0801	7092.8699	0.0000	1.0000
SYMI	41	-3407.9864	7099.7607	0.0000	1.0000
HKY	39	-3420.3830	7110.7108	0.0000	1.0000
GTR	43	-3407.1019	7111.8350	0.0000	1.0000
K2P	36	-3458.1582	7165.4961	0.0000	1.0000
F81G	39	-3451.6854	7173.3156	0.0000	1.0000
F81IG	40	-3450.9149	7178.6960	0.0000	1.0000
SYM	40	-3452.6313	7182.1289	0.0000	1.0000
F81I	39	-3457.1009	7184.1464	0.0000	1.0000
JC69G	36	-3480.8179	7210.8154	0.0000	1.0000
JC69IG	37	-3479.9580	7216.0174	0.0000	1.0000
JC69I	36	-3486.2421	7221.6639	0.0000	1.0000
F81	38	-3499.2958	7261.6145	0.0000	1.0000
JC69	35	-3529.7762	7301.8104	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/chr7_2669.phylip = 1 - 1014;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2669.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/chr7_2669.phylip = 1 - 1014;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2669.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/chr7_2669.phylip = 1 - 1014;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_2669.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

