
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:37 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/chr5_2978.phylip" (19 taxa, 378 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKY


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
HKYI	40	-850.4814	1790.6958	0.3697	0.3697
HKYG	40	-850.5151	1790.7632	0.3575	0.7272
HKYIG	41	-850.5237	1793.2973	0.1007	0.8278
HKY	39	-853.4045	1794.0398	0.0695	0.8973
GTRG	44	-847.6367	1795.1654	0.0396	0.9369
GTRI	44	-847.6656	1795.2230	0.0384	0.9753
GTR	43	-849.9874	1797.3041	0.0136	0.9889
GTRIG	45	-847.6340	1797.7379	0.0109	0.9998
F81I	39	-860.2034	1807.6376	0.0001	0.9999
F81G	39	-860.2141	1807.6590	0.0001	1.0000
F81IG	40	-860.2046	1810.1421	0.0000	1.0000
F81	38	-863.1894	1811.1222	0.0000	1.0000
K2PI	37	-875.9874	1834.2453	0.0000	1.0000
K2PG	37	-876.0878	1834.4462	0.0000	1.0000
K2PIG	38	-876.1140	1836.9713	0.0000	1.0000
SYMI	41	-872.5456	1837.3412	0.0000	1.0000
SYMG	41	-872.6238	1837.4976	0.0000	1.0000
K2P	36	-879.0661	1837.9445	0.0000	1.0000
SYM	40	-874.8982	1839.5294	0.0000	1.0000
SYMIG	42	-872.6310	1840.0442	0.0000	1.0000
JC69G	36	-883.9896	1847.7916	0.0000	1.0000
JC69I	36	-884.0285	1847.8693	0.0000	1.0000
JC69IG	37	-883.9817	1850.2339	0.0000	1.0000
JC69	35	-886.9763	1851.3209	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-850.4814	1780.9629	0.3044	0.3044
HKYG	40	-850.5151	1781.0303	0.2943	0.5988
HKYIG	41	-850.5237	1783.0473	0.1074	0.7061
GTRG	44	-847.6367	1783.2735	0.0959	0.8020
GTRI	44	-847.6656	1783.3311	0.0932	0.8952
HKY	39	-853.4045	1784.8091	0.0445	0.9397
GTRIG	45	-847.6340	1785.2681	0.0354	0.9750
GTR	43	-849.9874	1785.9747	0.0248	0.9999
F81I	39	-860.2034	1798.4068	0.0000	0.9999
F81G	39	-860.2141	1798.4282	0.0000	1.0000
F81IG	40	-860.2046	1800.4091	0.0000	1.0000
F81	38	-863.1894	1802.3789	0.0000	1.0000
K2PI	37	-875.9874	1825.9747	0.0000	1.0000
K2PG	37	-876.0878	1826.1757	0.0000	1.0000
SYMI	41	-872.5456	1827.0912	0.0000	1.0000
SYMG	41	-872.6238	1827.2476	0.0000	1.0000
K2PIG	38	-876.1140	1828.2279	0.0000	1.0000
SYMIG	42	-872.6310	1829.2621	0.0000	1.0000
SYM	40	-874.8982	1829.7965	0.0000	1.0000
K2P	36	-879.0661	1830.1321	0.0000	1.0000
JC69G	36	-883.9896	1839.9793	0.0000	1.0000
JC69I	36	-884.0285	1840.0570	0.0000	1.0000
JC69IG	37	-883.9817	1841.9633	0.0000	1.0000
JC69	35	-886.9763	1843.9525	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-853.4045	1938.2699	0.3410	0.3410
HKYI	40	-850.4814	1938.3586	0.3262	0.6672
HKYG	40	-850.5151	1938.4260	0.3154	0.9826
HKYIG	41	-850.5237	1944.3780	0.0161	0.9987
F81I	39	-860.2034	1951.8677	0.0004	0.9991
F81G	39	-860.2141	1951.8891	0.0004	0.9995
F81	38	-863.1894	1951.9048	0.0004	0.9998
GTR	43	-849.9874	1955.1752	0.0001	0.9999
GTRG	44	-847.6367	1956.4088	0.0000	0.9999
GTRI	44	-847.6656	1956.4664	0.0000	1.0000
F81IG	40	-860.2046	1957.8049	0.0000	1.0000
GTRIG	45	-847.6340	1962.3383	0.0000	1.0000
K2PI	37	-875.9874	1971.5658	0.0000	1.0000
K2PG	37	-876.0878	1971.7667	0.0000	1.0000
K2P	36	-879.0661	1971.7883	0.0000	1.0000
K2PIG	38	-876.1140	1977.7539	0.0000	1.0000
JC69G	36	-883.9896	1981.6355	0.0000	1.0000
JC69	35	-886.9763	1981.6738	0.0000	1.0000
JC69I	36	-884.0285	1981.7132	0.0000	1.0000
SYM	40	-874.8982	1987.1922	0.0000	1.0000
JC69IG	37	-883.9817	1987.5544	0.0000	1.0000
SYMI	41	-872.5456	1988.4218	0.0000	1.0000
SYMG	41	-872.6238	1988.5783	0.0000	1.0000
SYMIG	42	-872.6310	1994.5276	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2978.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2978.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2978.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2978.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (HKY)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2978.phylip = 1 - 378;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_2978.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

