
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:30 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_10096.phylip" (19 taxa, 328 characters)

Minimum AIC  model: GTRG
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	-987.3306	2066.0897	0.3029	0.3029
GTRG	44	-982.0548	2066.1024	0.3010	0.6039
HKYIG	41	-986.5580	2067.1580	0.1776	0.7815
GTRIG	45	-981.4778	2067.6366	0.1398	0.9213
HKYI	40	-989.3669	2070.1624	0.0395	0.9608
GTRI	44	-984.0947	2070.1824	0.0391	1.0000
K2PG	37	-1001.6911	2087.0788	0.0000	1.0000
K2PIG	38	-1000.7301	2087.7163	0.0000	1.0000
K2PI	37	-1003.4878	2090.6721	0.0000	1.0000
SYMG	41	-998.3395	2090.7210	0.0000	1.0000
SYMIG	42	-997.5478	2091.7693	0.0000	1.0000
SYMI	41	-999.8227	2093.6874	0.0000	1.0000
GTR	43	-998.3022	2095.9284	0.0000	1.0000
HKY	39	-1003.8535	2096.5404	0.0000	1.0000
F81G	39	-1010.8065	2110.4464	0.0000	1.0000
F81IG	40	-1009.9992	2111.4270	0.0000	1.0000
F81I	39	-1012.7548	2114.3430	0.0000	1.0000
K2P	36	-1019.2680	2119.6905	0.0000	1.0000
SYM	40	-1015.7245	2122.8776	0.0000	1.0000
JC69G	36	-1023.3910	2127.9367	0.0000	1.0000
JC69IG	37	-1022.5205	2128.7375	0.0000	1.0000
JC69I	36	-1025.2034	2131.5614	0.0000	1.0000
F81	38	-1027.1476	2140.5512	0.0000	1.0000
JC69	35	-1040.2681	2159.1664	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-982.0548	2052.1095	0.4305	0.4305
GTRIG	45	-981.4778	2052.9557	0.2820	0.7124
HKYG	40	-987.3306	2054.6611	0.1202	0.8326
HKYIG	41	-986.5580	2055.1160	0.0957	0.9283
GTRI	44	-984.0947	2056.1895	0.0560	0.9843
HKYI	40	-989.3669	2058.7339	0.0157	1.0000
K2PG	37	-1001.6911	2077.3822	0.0000	1.0000
K2PIG	38	-1000.7301	2077.4602	0.0000	1.0000
SYMG	41	-998.3395	2078.6790	0.0000	1.0000
SYMIG	42	-997.5478	2079.0956	0.0000	1.0000
K2PI	37	-1003.4878	2080.9755	0.0000	1.0000
SYMI	41	-999.8227	2081.6455	0.0000	1.0000
GTR	43	-998.3022	2082.6045	0.0000	1.0000
HKY	39	-1003.8535	2085.7071	0.0000	1.0000
F81G	39	-1010.8065	2099.6130	0.0000	1.0000
F81IG	40	-1009.9992	2099.9984	0.0000	1.0000
F81I	39	-1012.7548	2103.5096	0.0000	1.0000
K2P	36	-1019.2680	2110.5359	0.0000	1.0000
SYM	40	-1015.7245	2111.4490	0.0000	1.0000
JC69G	36	-1023.3910	2118.7820	0.0000	1.0000
JC69IG	37	-1022.5205	2119.0410	0.0000	1.0000
JC69I	36	-1025.2034	2122.4068	0.0000	1.0000
F81	38	-1027.1476	2130.2951	0.0000	1.0000
JC69	35	-1040.2681	2150.5363	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-987.3306	2206.3817	0.7957	0.7957
HKYI	40	-989.3669	2210.4544	0.1038	0.8995
HKYIG	41	-986.5580	2210.6296	0.0951	0.9946
K2PG	37	-1001.6911	2217.7237	0.0027	0.9974
GTRG	44	-982.0548	2219.0021	0.0014	0.9988
K2PI	37	-1003.4878	2221.3170	0.0005	0.9993
K2PIG	38	-1000.7301	2221.5948	0.0004	0.9997
GTRI	44	-984.0947	2223.0821	0.0002	0.9999
GTRIG	45	-981.4778	2223.6413	0.0001	1.0000
HKY	39	-1003.8535	2233.6346	0.0000	1.0000
SYMG	41	-998.3395	2234.1926	0.0000	1.0000
SYMI	41	-999.8227	2237.1590	0.0000	1.0000
SYMIG	42	-997.5478	2238.4022	0.0000	1.0000
GTR	43	-998.3022	2245.7040	0.0000	1.0000
K2P	36	-1019.2680	2247.0844	0.0000	1.0000
F81G	39	-1010.8065	2247.5406	0.0000	1.0000
F81I	39	-1012.7548	2251.4372	0.0000	1.0000
F81IG	40	-1009.9992	2251.7189	0.0000	1.0000
JC69G	36	-1023.3910	2255.3305	0.0000	1.0000
JC69I	36	-1025.2034	2258.9553	0.0000	1.0000
JC69IG	37	-1022.5205	2259.3825	0.0000	1.0000
SYM	40	-1015.7245	2263.1695	0.0000	1.0000
F81	38	-1027.1476	2274.4297	0.0000	1.0000
JC69	35	-1040.2681	2283.2918	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/chr5_10096.phylip = 1 - 328;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10096.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 (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10096.phylip = 1 - 328;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10096.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/chr5_10096.phylip = 1 - 328;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10096.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;


-------------------------------------------------------------
End of Output

