
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:28 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_7251.phylip" (19 taxa, 549 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	-1911.6376	3909.7320	0.4392	0.4392
GTRG	44	-1907.7938	3911.4448	0.1865	0.6257
HKYIG	41	-1911.6161	3912.0250	0.1395	0.7652
HKYI	40	-1912.8888	3912.2343	0.1257	0.8909
GTRIG	45	-1907.7826	3913.7958	0.0576	0.9485
GTRI	44	-1909.0808	3914.0187	0.0515	1.0000
K2PG	37	-1930.7399	3940.9828	0.0000	1.0000
K2PI	37	-1931.8682	3943.2394	0.0000	1.0000
K2PIG	38	-1930.7204	3943.2525	0.0000	1.0000
SYMG	41	-1929.3724	3947.5378	0.0000	1.0000
SYMI	41	-1930.4619	3949.7167	0.0000	1.0000
SYMIG	42	-1929.3608	3949.8598	0.0000	1.0000
HKY	39	-1932.8787	3949.8871	0.0000	1.0000
GTR	43	-1930.0017	3953.4966	0.0000	1.0000
K2P	36	-1949.9425	3977.0881	0.0000	1.0000
SYM	40	-1948.4917	3983.4402	0.0000	1.0000
F81G	39	-1965.0487	4014.2271	0.0000	1.0000
F81I	39	-1965.5761	4015.2818	0.0000	1.0000
F81IG	40	-1964.6357	4015.7280	0.0000	1.0000
JC69G	36	-1978.9652	4035.1335	0.0000	1.0000
JC69I	36	-1979.1099	4035.4229	0.0000	1.0000
JC69IG	37	-1978.4834	4036.4698	0.0000	1.0000
F81	38	-1984.0161	4049.8440	0.0000	1.0000
JC69	35	-1995.8672	4066.6467	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1911.6376	3903.2753	0.3255	0.3255
GTRG	44	-1907.7938	3903.5877	0.2785	0.6040
HKYIG	41	-1911.6161	3905.2321	0.1224	0.7264
GTRIG	45	-1907.7826	3905.5652	0.1036	0.8300
HKYI	40	-1912.8888	3905.7776	0.0932	0.9231
GTRI	44	-1909.0808	3906.1615	0.0769	1.0000
K2PG	37	-1930.7399	3935.4799	0.0000	1.0000
K2PIG	38	-1930.7204	3937.4407	0.0000	1.0000
K2PI	37	-1931.8682	3937.7365	0.0000	1.0000
SYMG	41	-1929.3724	3940.7449	0.0000	1.0000
SYMIG	42	-1929.3608	3942.7215	0.0000	1.0000
SYMI	41	-1930.4619	3942.9238	0.0000	1.0000
HKY	39	-1932.8787	3943.7574	0.0000	1.0000
GTR	43	-1930.0017	3946.0035	0.0000	1.0000
K2P	36	-1949.9425	3971.8850	0.0000	1.0000
SYM	40	-1948.4917	3976.9835	0.0000	1.0000
F81G	39	-1965.0487	4008.0974	0.0000	1.0000
F81I	39	-1965.5761	4009.1521	0.0000	1.0000
F81IG	40	-1964.6357	4009.2713	0.0000	1.0000
JC69G	36	-1978.9652	4029.9303	0.0000	1.0000
JC69I	36	-1979.1099	4030.2197	0.0000	1.0000
JC69IG	37	-1978.4834	4030.9669	0.0000	1.0000
F81	38	-1984.0161	4044.0323	0.0000	1.0000
JC69	35	-1995.8672	4061.7344	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1911.6376	4075.5992	0.7518	0.7518
HKYI	40	-1912.8888	4078.1016	0.2152	0.9670
HKYIG	41	-1911.6161	4081.8642	0.0328	0.9998
GTRG	44	-1907.7938	4093.1440	0.0001	0.9999
K2PG	37	-1930.7399	4094.8795	0.0000	0.9999
GTRI	44	-1909.0808	4095.7179	0.0000	1.0000
K2PI	37	-1931.8682	4097.1361	0.0000	1.0000
GTRIG	45	-1907.7826	4099.4296	0.0000	1.0000
K2PIG	38	-1930.7204	4101.1485	0.0000	1.0000
HKY	39	-1932.8787	4111.7732	0.0000	1.0000
SYMG	41	-1929.3724	4117.3769	0.0000	1.0000
SYMI	41	-1930.4619	4119.5558	0.0000	1.0000
SYMIG	42	-1929.3608	4123.6616	0.0000	1.0000
K2P	36	-1949.9425	4126.9765	0.0000	1.0000
GTR	43	-1930.0017	4131.2517	0.0000	1.0000
SYM	40	-1948.4917	4149.3074	0.0000	1.0000
F81G	39	-1965.0487	4176.1133	0.0000	1.0000
F81I	39	-1965.5761	4177.1680	0.0000	1.0000
F81IG	40	-1964.6357	4181.5953	0.0000	1.0000
JC69G	36	-1978.9652	4185.0219	0.0000	1.0000
JC69I	36	-1979.1099	4185.3113	0.0000	1.0000
JC69IG	37	-1978.4834	4190.3665	0.0000	1.0000
F81	38	-1984.0161	4207.7400	0.0000	1.0000
JC69	35	-1995.8672	4212.5178	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_7251.phylip = 1 - 549;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7251.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_7251.phylip = 1 - 549;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7251.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_7251.phylip = 1 - 549;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_7251.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

