
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:52 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/chr3_2737.phylip" (19 taxa, 392 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
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
HKYG	40	-965.9767	2021.2982	0.4508	0.4508
HKYI	40	-966.4976	2022.3399	0.2678	0.7186
HKYIG	41	-965.3625	2022.5649	0.2393	0.9579
GTRG	44	-964.0710	2027.5542	0.0197	0.9776
GTRIG	45	-963.3545	2028.6742	0.0113	0.9889
GTRI	44	-964.7234	2028.8589	0.0103	0.9992
K2PG	37	-976.7829	2035.5093	0.0004	0.9995
K2PI	37	-977.2218	2036.3871	0.0002	0.9998
K2PIG	38	-976.2538	2036.9042	0.0002	1.0000
SYMG	41	-975.4330	2042.7059	0.0000	1.0000
SYMI	41	-975.9011	2043.6422	0.0000	1.0000
SYMIG	42	-974.8653	2044.0803	0.0000	1.0000
HKY	39	-979.1800	2045.2236	0.0000	1.0000
F81G	39	-979.3801	2045.6238	0.0000	1.0000
F81I	39	-979.8471	2046.5578	0.0000	1.0000
F81IG	40	-978.9184	2047.1814	0.0000	1.0000
GTR	43	-977.2360	2051.3457	0.0000	1.0000
JC69G	36	-989.0926	2057.6894	0.0000	1.0000
JC69I	36	-989.5272	2058.5586	0.0000	1.0000
JC69IG	37	-988.6534	2059.2502	0.0000	1.0000
K2P	36	-990.1004	2059.7051	0.0000	1.0000
SYM	40	-988.7188	2066.7823	0.0000	1.0000
F81	38	-992.2334	2068.8633	0.0000	1.0000
JC69	35	-1001.9916	2081.0618	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-965.9767	2011.9535	0.3914	0.3914
HKYIG	41	-965.3625	2012.7249	0.2661	0.6575
HKYI	40	-966.4976	2012.9952	0.2325	0.8900
GTRG	44	-964.0710	2016.1421	0.0482	0.9382
GTRIG	45	-963.3545	2016.7089	0.0363	0.9745
GTRI	44	-964.7234	2017.4468	0.0251	0.9996
K2PG	37	-976.7829	2027.5658	0.0002	0.9998
K2PI	37	-977.2218	2028.4436	0.0001	0.9999
K2PIG	38	-976.2538	2028.5076	0.0001	1.0000
SYMG	41	-975.4330	2032.8659	0.0000	1.0000
SYMIG	42	-974.8653	2033.7307	0.0000	1.0000
SYMI	41	-975.9011	2033.8022	0.0000	1.0000
HKY	39	-979.1800	2036.3600	0.0000	1.0000
F81G	39	-979.3801	2036.7601	0.0000	1.0000
F81I	39	-979.8471	2037.6942	0.0000	1.0000
F81IG	40	-978.9184	2037.8367	0.0000	1.0000
GTR	43	-977.2360	2040.4721	0.0000	1.0000
JC69G	36	-989.0926	2050.1851	0.0000	1.0000
JC69I	36	-989.5272	2051.0543	0.0000	1.0000
JC69IG	37	-988.6534	2051.3067	0.0000	1.0000
K2P	36	-990.1004	2052.2008	0.0000	1.0000
SYM	40	-988.7188	2057.4376	0.0000	1.0000
F81	38	-992.2334	2060.4667	0.0000	1.0000
JC69	35	-1001.9916	2073.9831	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-965.9767	2170.8039	0.5102	0.5102
HKYI	40	-966.4976	2171.8457	0.3031	0.8133
K2PG	37	-976.7829	2174.5024	0.0803	0.8936
K2PI	37	-977.2218	2175.3802	0.0518	0.9454
HKYIG	41	-965.3625	2175.5467	0.0476	0.9930
K2PIG	38	-976.2538	2179.4155	0.0069	0.9999
GTRG	44	-964.0710	2190.8776	0.0000	0.9999
HKY	39	-979.1800	2191.2392	0.0000	0.9999
F81G	39	-979.3801	2191.6394	0.0000	1.0000
GTRI	44	-964.7234	2192.1823	0.0000	1.0000
F81I	39	-979.8471	2192.5734	0.0000	1.0000
JC69G	36	-989.0926	2193.1506	0.0000	1.0000
JC69I	36	-989.5272	2194.0198	0.0000	1.0000
K2P	36	-990.1004	2195.1663	0.0000	1.0000
GTRIG	45	-963.3545	2195.4157	0.0000	1.0000
SYMG	41	-975.4330	2195.6876	0.0000	1.0000
SYMI	41	-975.9011	2196.6240	0.0000	1.0000
F81IG	40	-978.9184	2196.6872	0.0000	1.0000
JC69IG	37	-988.6534	2198.2434	0.0000	1.0000
SYMIG	42	-974.8653	2200.5237	0.0000	1.0000
GTR	43	-977.2360	2211.2364	0.0000	1.0000
F81	38	-992.2334	2211.3747	0.0000	1.0000
JC69	35	-1001.9916	2212.9773	0.0000	1.0000
SYM	40	-988.7188	2216.2881	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/chr3_2737.phylip = 1 - 392;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2737.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/chr3_2737.phylip = 1 - 392;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2737.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2737.phylip = 1 - 392;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_2737.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

