
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:06 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_4670.phylip" (19 taxa, 675 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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	-1861.1420	3807.4575	0.4467	0.4467
HKYI	40	-1861.5198	3808.2131	0.3062	0.7528
HKYIG	41	-1861.1469	3809.7345	0.1431	0.8959
GTRG	44	-1858.9559	3812.1974	0.0418	0.9377
GTRI	44	-1859.2622	3812.8101	0.0307	0.9684
GTRIG	45	-1858.9676	3814.5171	0.0131	0.9815
K2PG	37	-1868.6351	3815.6847	0.0073	0.9888
K2PI	37	-1869.1150	3816.6444	0.0045	0.9933
HKY	39	-1867.3786	3817.6705	0.0027	0.9960
K2PIG	38	-1868.6359	3817.9321	0.0024	0.9984
SYMG	41	-1866.6786	3820.7980	0.0006	0.9990
GTR	43	-1864.6381	3821.2730	0.0004	0.9994
SYMI	41	-1867.1143	3821.6694	0.0004	0.9998
SYMIG	42	-1866.6971	3823.1094	0.0002	1.0000
K2P	36	-1874.9403	3826.0561	0.0000	1.0000
SYM	40	-1872.2896	3829.7528	0.0000	1.0000
F81G	39	-1896.9766	3876.8666	0.0000	1.0000
F81I	39	-1897.6183	3878.1500	0.0000	1.0000
F81IG	40	-1896.9937	3879.1609	0.0000	1.0000
JC69G	36	-1903.9171	3884.0098	0.0000	1.0000
JC69I	36	-1904.5970	3885.3694	0.0000	1.0000
F81	38	-1902.5086	3885.6776	0.0000	1.0000
JC69IG	37	-1903.9342	3886.2829	0.0000	1.0000
JC69	35	-1909.4874	3892.9185	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1861.1420	3802.2840	0.4122	0.4122
HKYI	40	-1861.5198	3803.0396	0.2825	0.6948
HKYIG	41	-1861.1469	3804.2937	0.1509	0.8457
GTRG	44	-1858.9559	3805.9117	0.0672	0.9129
GTRI	44	-1859.2622	3806.5244	0.0495	0.9624
GTRIG	45	-1858.9676	3807.9352	0.0244	0.9868
K2PG	37	-1868.6351	3811.2703	0.0046	0.9914
K2PI	37	-1869.1150	3812.2300	0.0029	0.9943
HKY	39	-1867.3786	3812.7572	0.0022	0.9965
K2PIG	38	-1868.6359	3813.2717	0.0017	0.9981
GTR	43	-1864.6381	3815.2761	0.0006	0.9988
SYMG	41	-1866.6786	3815.3572	0.0006	0.9994
SYMI	41	-1867.1143	3816.2287	0.0004	0.9998
SYMIG	42	-1866.6971	3817.3942	0.0002	1.0000
K2P	36	-1874.9403	3821.8805	0.0000	1.0000
SYM	40	-1872.2896	3824.5793	0.0000	1.0000
F81G	39	-1896.9766	3871.9532	0.0000	1.0000
F81I	39	-1897.6183	3873.2366	0.0000	1.0000
F81IG	40	-1896.9937	3873.9874	0.0000	1.0000
JC69G	36	-1903.9171	3879.8342	0.0000	1.0000
F81	38	-1902.5086	3881.0172	0.0000	1.0000
JC69I	36	-1904.5970	3881.1939	0.0000	1.0000
JC69IG	37	-1903.9342	3881.8685	0.0000	1.0000
JC69	35	-1909.4874	3888.9748	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1868.6351	3978.3146	0.5301	0.5301
K2PI	37	-1869.1150	3979.2743	0.3281	0.8581
HKYG	40	-1861.1420	3982.8725	0.0543	0.9124
HKYI	40	-1861.5198	3983.6281	0.0372	0.9496
K2P	36	-1874.9403	3984.4102	0.0252	0.9748
K2PIG	38	-1868.6359	3984.8308	0.0204	0.9951
HKY	39	-1867.3786	3988.8310	0.0028	0.9979
HKYIG	41	-1861.1469	3989.3969	0.0021	1.0000
SYMG	41	-1866.6786	4000.4605	0.0000	1.0000
SYMI	41	-1867.1143	4001.3319	0.0000	1.0000
GTRG	44	-1858.9559	4004.5591	0.0000	1.0000
SYM	40	-1872.2896	4005.1678	0.0000	1.0000
GTRI	44	-1859.2622	4005.1717	0.0000	1.0000
SYMIG	42	-1866.6971	4007.0122	0.0000	1.0000
GTR	43	-1864.6381	4009.4088	0.0000	1.0000
GTRIG	45	-1858.9676	4011.0973	0.0000	1.0000
JC69G	36	-1903.9171	4042.3639	0.0000	1.0000
JC69I	36	-1904.5970	4043.7236	0.0000	1.0000
JC69	35	-1909.4874	4046.9897	0.0000	1.0000
F81G	39	-1896.9766	4048.0270	0.0000	1.0000
JC69IG	37	-1903.9342	4048.9128	0.0000	1.0000
F81I	39	-1897.6183	4049.3104	0.0000	1.0000
F81	38	-1902.5086	4052.5763	0.0000	1.0000
F81IG	40	-1896.9937	4054.5759	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/chr7_4670.phylip = 1 - 675;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4670.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/chr7_4670.phylip = 1 - 675;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4670.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4670.phylip = 1 - 675;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_4670.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

