
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:14 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_4941.phylip" (19 taxa, 687 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	-1815.0225	3724.2133	0.3374	0.3374
HKYG	40	-1820.0197	3725.1167	0.2147	0.5521
GTRIG	45	-1814.3848	3725.2283	0.2031	0.7552
HKYIG	41	-1819.4181	3726.1758	0.1265	0.8817
GTRI	44	-1816.5438	3727.2559	0.0737	0.9554
HKYI	40	-1821.5906	3728.2585	0.0446	1.0000
HKY	39	-1841.7525	3766.3273	0.0000	1.0000
GTR	43	-1838.2048	3768.2944	0.0000	1.0000
K2PG	37	-1855.1852	3788.7031	0.0000	1.0000
K2PIG	38	-1854.6122	3789.7985	0.0000	1.0000
SYMG	41	-1852.0075	3791.3546	0.0000	1.0000
K2PI	37	-1856.7129	3791.7587	0.0000	1.0000
SYMIG	42	-1851.4287	3792.4661	0.0000	1.0000
SYMI	41	-1853.4587	3794.2570	0.0000	1.0000
F81G	39	-1865.8529	3814.5281	0.0000	1.0000
F81IG	40	-1865.3555	3815.7885	0.0000	1.0000
F81I	39	-1867.3527	3817.5277	0.0000	1.0000
K2P	36	-1875.9908	3828.0801	0.0000	1.0000
SYM	40	-1873.3944	3831.8662	0.0000	1.0000
F81	38	-1886.2032	3852.9804	0.0000	1.0000
JC69G	36	-1895.0531	3866.2047	0.0000	1.0000
JC69IG	37	-1894.5521	3867.4370	0.0000	1.0000
JC69I	36	-1896.5541	3869.2066	0.0000	1.0000
JC69	35	-1915.2510	3904.3729	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1815.0225	3718.0450	0.3835	0.3835
GTRIG	45	-1814.3848	3718.7697	0.2669	0.6504
HKYG	40	-1820.0197	3720.0393	0.1415	0.7919
HKYIG	41	-1819.4181	3720.8362	0.0950	0.8868
GTRI	44	-1816.5438	3721.0877	0.0838	0.9706
HKYI	40	-1821.5906	3723.1811	0.0294	1.0000
HKY	39	-1841.7525	3761.5050	0.0000	1.0000
GTR	43	-1838.2048	3762.4095	0.0000	1.0000
K2PG	37	-1855.1852	3784.3703	0.0000	1.0000
K2PIG	38	-1854.6122	3785.2244	0.0000	1.0000
SYMG	41	-1852.0075	3786.0151	0.0000	1.0000
SYMIG	42	-1851.4287	3786.8574	0.0000	1.0000
K2PI	37	-1856.7129	3787.4258	0.0000	1.0000
SYMI	41	-1853.4587	3788.9174	0.0000	1.0000
F81G	39	-1865.8529	3809.7059	0.0000	1.0000
F81IG	40	-1865.3555	3810.7111	0.0000	1.0000
F81I	39	-1867.3527	3812.7055	0.0000	1.0000
K2P	36	-1875.9908	3823.9816	0.0000	1.0000
SYM	40	-1873.3944	3826.7888	0.0000	1.0000
F81	38	-1886.2032	3848.4063	0.0000	1.0000
JC69G	36	-1895.0531	3862.1062	0.0000	1.0000
JC69IG	37	-1894.5521	3863.1042	0.0000	1.0000
JC69I	36	-1896.5541	3865.1082	0.0000	1.0000
JC69	35	-1915.2510	3900.5020	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1820.0197	3901.3327	0.7825	0.7825
HKYI	40	-1821.5906	3904.4745	0.1627	0.9452
HKYIG	41	-1819.4181	3906.6619	0.0545	0.9997
GTRG	44	-1815.0225	3917.4677	0.0002	0.9999
GTRI	44	-1816.5438	3920.5104	0.0001	1.0000
GTRIG	45	-1814.3848	3922.7247	0.0000	1.0000
HKY	39	-1841.7525	3938.2661	0.0000	1.0000
K2PG	37	-1855.1852	3952.0667	0.0000	1.0000
K2PI	37	-1856.7129	3955.1222	0.0000	1.0000
GTR	43	-1838.2048	3957.2999	0.0000	1.0000
K2PIG	38	-1854.6122	3957.4531	0.0000	1.0000
SYMG	41	-1852.0075	3971.8408	0.0000	1.0000
SYMI	41	-1853.4587	3974.7431	0.0000	1.0000
SYMIG	42	-1851.4287	3977.2154	0.0000	1.0000
F81G	39	-1865.8529	3986.4669	0.0000	1.0000
K2P	36	-1875.9908	3987.1456	0.0000	1.0000
F81I	39	-1867.3527	3989.4665	0.0000	1.0000
F81IG	40	-1865.3555	3992.0045	0.0000	1.0000
SYM	40	-1873.3944	4008.0822	0.0000	1.0000
F81	38	-1886.2032	4020.6350	0.0000	1.0000
JC69G	36	-1895.0531	4025.2702	0.0000	1.0000
JC69I	36	-1896.5541	4028.2722	0.0000	1.0000
JC69IG	37	-1894.5521	4030.8006	0.0000	1.0000
JC69	35	-1915.2510	4059.1337	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_4941.phylip = 1 - 687;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4941.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_4941.phylip = 1 - 687;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4941.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_4941.phylip = 1 - 687;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4941.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

