
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:23 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/chr11_3190.phylip" (19 taxa, 641 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	-1913.3563	3921.3569	0.9039	0.9039
HKYG	40	-1920.1917	3925.8500	0.0956	0.9995
GTRIG	45	-1920.6151	3938.1882	0.0002	0.9997
HKYIG	41	-1925.8651	3939.4798	0.0001	0.9998
GTRI	44	-1922.5575	3939.7594	0.0001	0.9999
HKYI	40	-1927.3452	3940.1570	0.0001	1.0000
GTR	43	-1932.1107	3956.5597	0.0000	1.0000
HKY	39	-1937.5347	3958.2608	0.0000	1.0000
SYMG	41	-1937.2828	3962.3153	0.0000	1.0000
K2PG	37	-1943.0331	3964.7295	0.0000	1.0000
SYMIG	42	-1943.7048	3977.4498	0.0000	1.0000
SYMI	41	-1945.3327	3978.4150	0.0000	1.0000
K2PIG	38	-1948.8555	3978.6347	0.0000	1.0000
K2PI	37	-1950.3335	3979.3304	0.0000	1.0000
F81G	39	-1951.4112	3986.0137	0.0000	1.0000
SYM	40	-1953.4995	3992.4657	0.0000	1.0000
K2P	36	-1959.4207	3995.2520	0.0000	1.0000
F81I	39	-1956.0465	3995.2842	0.0000	1.0000
F81IG	40	-1958.3199	4002.1065	0.0000	1.0000
JC69G	36	-1970.7532	4017.9170	0.0000	1.0000
F81	38	-1969.5437	4020.0109	0.0000	1.0000
JC69I	36	-1975.2922	4026.9951	0.0000	1.0000
JC69IG	37	-1977.8801	4034.4236	0.0000	1.0000
JC69	35	-1987.8223	4049.8099	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1913.3563	3914.7126	0.9441	0.9441
HKYG	40	-1920.1917	3920.3834	0.0554	0.9995
GTRIG	45	-1920.6151	3931.2302	0.0002	0.9998
GTRI	44	-1922.5575	3933.1151	0.0001	0.9999
HKYIG	41	-1925.8651	3933.7303	0.0001	1.0000
HKYI	40	-1927.3452	3934.6904	0.0000	1.0000
GTR	43	-1932.1107	3950.2214	0.0000	1.0000
HKY	39	-1937.5347	3953.0695	0.0000	1.0000
SYMG	41	-1937.2828	3956.5657	0.0000	1.0000
K2PG	37	-1943.0331	3960.0662	0.0000	1.0000
SYMIG	42	-1943.7048	3971.4096	0.0000	1.0000
SYMI	41	-1945.3327	3972.6655	0.0000	1.0000
K2PIG	38	-1948.8555	3973.7111	0.0000	1.0000
K2PI	37	-1950.3335	3974.6670	0.0000	1.0000
F81G	39	-1951.4112	3980.8224	0.0000	1.0000
SYM	40	-1953.4995	3986.9991	0.0000	1.0000
F81I	39	-1956.0465	3990.0929	0.0000	1.0000
K2P	36	-1959.4207	3990.8414	0.0000	1.0000
F81IG	40	-1958.3199	3996.6398	0.0000	1.0000
JC69G	36	-1970.7532	4013.5064	0.0000	1.0000
F81	38	-1969.5437	4015.0873	0.0000	1.0000
JC69I	36	-1975.2922	4022.5845	0.0000	1.0000
JC69IG	37	-1977.8801	4029.7603	0.0000	1.0000
JC69	35	-1987.8223	4045.6446	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1920.1917	4098.9046	0.9968	0.9968
GTRG	44	-1913.3563	4111.0859	0.0023	0.9991
HKYI	40	-1927.3452	4113.2115	0.0008	0.9999
HKYIG	41	-1925.8651	4116.7145	0.0001	1.0000
K2PG	37	-1943.0331	4125.1983	0.0000	1.0000
HKY	39	-1937.5347	4127.1276	0.0000	1.0000
GTRI	44	-1922.5575	4129.4884	0.0000	1.0000
GTRIG	45	-1920.6151	4132.0665	0.0000	1.0000
SYMG	41	-1937.2828	4139.5499	0.0000	1.0000
K2PI	37	-1950.3335	4139.7991	0.0000	1.0000
GTR	43	-1932.1107	4142.1316	0.0000	1.0000
K2PIG	38	-1948.8555	4143.3062	0.0000	1.0000
K2P	36	-1959.4207	4151.5104	0.0000	1.0000
F81G	39	-1951.4112	4154.8805	0.0000	1.0000
SYMI	41	-1945.3327	4155.6497	0.0000	1.0000
SYMIG	42	-1943.7048	4158.8569	0.0000	1.0000
F81I	39	-1956.0465	4164.1510	0.0000	1.0000
SYM	40	-1953.4995	4165.5202	0.0000	1.0000
JC69G	36	-1970.7532	4174.1755	0.0000	1.0000
F81IG	40	-1958.3199	4175.1610	0.0000	1.0000
JC69I	36	-1975.2922	4183.2536	0.0000	1.0000
F81	38	-1969.5437	4184.6824	0.0000	1.0000
JC69IG	37	-1977.8801	4194.8923	0.0000	1.0000
JC69	35	-1987.8223	4201.8506	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/chr11_3190.phylip = 1 - 641;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3190.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/chr11_3190.phylip = 1 - 641;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3190.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/chr11_3190.phylip = 1 - 641;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3190.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

