
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:01 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/chr13_2779.phylip" (19 taxa, 636 characters)

Minimum AIC  model: GTRIG
Minimum AICc model: GTRIG
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
GTRIG	45	-1953.3521	4003.7211	0.3793	0.3793
HKYIG	41	-1958.2053	4004.2086	0.2972	0.6765
HKYG	40	-1959.9779	4005.4683	0.1583	0.8348
GTRG	44	-1955.4580	4005.6165	0.1470	0.9819
HKYI	40	-1962.6201	4010.7529	0.0113	0.9931
GTRI	44	-1958.5229	4011.7462	0.0069	1.0000
F81IG	40	-2000.4016	4086.3158	0.0000	1.0000
F81G	39	-2001.5724	4086.3797	0.0000	1.0000
F81I	39	-2003.0947	4089.4243	0.0000	1.0000
K2PIG	38	-2007.7605	4096.4859	0.0000	1.0000
K2PG	37	-2009.0192	4096.7408	0.0000	1.0000
K2PI	37	-2010.8483	4100.3989	0.0000	1.0000
SYMIG	42	-2007.4160	4104.9231	0.0000	1.0000
SYMG	41	-2008.7659	4105.3297	0.0000	1.0000
SYMI	41	-2010.6111	4109.0202	0.0000	1.0000
HKY	39	-2013.3684	4109.9716	0.0000	1.0000
GTR	43	-2009.5179	4111.4277	0.0000	1.0000
JC69G	36	-2045.0037	4166.4547	0.0000	1.0000
JC69IG	37	-2044.1928	4167.0880	0.0000	1.0000
JC69I	36	-2046.6125	4169.6723	0.0000	1.0000
F81	38	-2052.4990	4185.9627	0.0000	1.0000
K2P	36	-2061.0827	4198.6128	0.0000	1.0000
SYM	40	-2060.8291	4207.1708	0.0000	1.0000
JC69	35	-2094.9691	4264.1383	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-1953.3521	3996.7042	0.5042	0.5042
HKYIG	41	-1958.2053	3998.4106	0.2148	0.7191
GTRG	44	-1955.4580	3998.9160	0.1669	0.8859
HKYG	40	-1959.9779	3999.9557	0.0992	0.9852
GTRI	44	-1958.5229	4005.0457	0.0078	0.9929
HKYI	40	-1962.6201	4005.2403	0.0071	1.0000
F81IG	40	-2000.4016	4080.8032	0.0000	1.0000
F81G	39	-2001.5724	4081.1448	0.0000	1.0000
F81I	39	-2003.0947	4084.1894	0.0000	1.0000
K2PIG	38	-2007.7605	4091.5211	0.0000	1.0000
K2PG	37	-2009.0192	4092.0385	0.0000	1.0000
K2PI	37	-2010.8483	4095.6965	0.0000	1.0000
SYMIG	42	-2007.4160	4098.8321	0.0000	1.0000
SYMG	41	-2008.7659	4099.5317	0.0000	1.0000
SYMI	41	-2010.6111	4103.2222	0.0000	1.0000
HKY	39	-2013.3684	4104.7367	0.0000	1.0000
GTR	43	-2009.5179	4105.0358	0.0000	1.0000
JC69G	36	-2045.0037	4162.0073	0.0000	1.0000
JC69IG	37	-2044.1928	4162.3856	0.0000	1.0000
JC69I	36	-2046.6125	4165.2249	0.0000	1.0000
F81	38	-2052.4990	4180.9979	0.0000	1.0000
K2P	36	-2061.0827	4194.1653	0.0000	1.0000
SYM	40	-2060.8291	4201.6582	0.0000	1.0000
JC69	35	-2094.9691	4259.9383	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1959.9779	4178.1637	0.7663	0.7663
HKYIG	41	-1958.2053	4181.0738	0.1789	0.9452
HKYI	40	-1962.6201	4183.4482	0.0546	0.9998
GTRG	44	-1955.4580	4194.9447	0.0002	0.9999
GTRIG	45	-1953.3521	4197.1881	0.0001	1.0000
GTRI	44	-1958.5229	4201.0745	0.0000	1.0000
F81G	39	-2001.5724	4254.8975	0.0000	1.0000
K2PG	37	-2009.0192	4256.8808	0.0000	1.0000
F81I	39	-2003.0947	4257.9421	0.0000	1.0000
F81IG	40	-2000.4016	4259.0111	0.0000	1.0000
K2PI	37	-2010.8483	4260.5389	0.0000	1.0000
K2PIG	38	-2007.7605	4260.8186	0.0000	1.0000
HKY	39	-2013.3684	4278.4895	0.0000	1.0000
SYMG	41	-2008.7659	4282.1949	0.0000	1.0000
SYMI	41	-2010.6111	4285.8854	0.0000	1.0000
SYMIG	42	-2007.4160	4285.9504	0.0000	1.0000
GTR	43	-2009.5179	4296.6093	0.0000	1.0000
JC69G	36	-2045.0037	4322.3945	0.0000	1.0000
JC69I	36	-2046.6125	4325.6121	0.0000	1.0000
JC69IG	37	-2044.1928	4327.2280	0.0000	1.0000
F81	38	-2052.4990	4350.2954	0.0000	1.0000
K2P	36	-2061.0827	4354.5525	0.0000	1.0000
SYM	40	-2060.8291	4379.8661	0.0000	1.0000
JC69	35	-2094.9691	4415.8702	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2779.phylip = 1 - 636;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2779.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2779.phylip = 1 - 636;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2779.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
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/chr13_2779.phylip = 1 - 636;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_2779.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

