
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:32 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/chr1_5492.phylip" (19 taxa, 862 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	-4081.5883	8256.0237	0.8084	0.8084
GTRIG	45	-4081.9213	8258.9161	0.1903	0.9987
HKYG	40	-4092.7418	8269.4787	0.0010	0.9997
HKYIG	41	-4092.7417	8271.6833	0.0003	1.0000
GTRI	44	-4097.2907	8287.4284	0.0000	1.0000
HKYI	40	-4108.1858	8300.3666	0.0000	1.0000
GTR	43	-4176.7635	8444.1530	0.0000	1.0000
HKY	39	-4183.9280	8449.6516	0.0000	1.0000
SYMG	41	-4186.1085	8458.4171	0.0000	1.0000
SYMIG	42	-4186.1084	8460.6270	0.0000	1.0000
K2PG	37	-4193.4854	8464.3834	0.0000	1.0000
K2PIG	38	-4193.4853	8466.5720	0.0000	1.0000
F81G	39	-4193.3861	8468.5678	0.0000	1.0000
F81IG	40	-4198.5269	8481.0489	0.0000	1.0000
F81I	39	-4205.2653	8492.3262	0.0000	1.0000
SYMI	41	-4203.6069	8493.4137	0.0000	1.0000
K2PI	37	-4209.5939	8496.6005	0.0000	1.0000
JC69G	36	-4270.2711	8615.7713	0.0000	1.0000
JC69IG	37	-4274.8101	8627.0328	0.0000	1.0000
F81	38	-4280.0509	8639.7033	0.0000	1.0000
SYM	40	-4278.1577	8640.3105	0.0000	1.0000
JC69I	36	-4284.2268	8643.6827	0.0000	1.0000
K2P	36	-4287.0214	8649.2720	0.0000	1.0000
JC69	35	-4357.7865	8788.6239	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4081.5883	8251.1767	0.7907	0.7907
GTRIG	45	-4081.9213	8253.8425	0.2085	0.9992
HKYG	40	-4092.7418	8265.4836	0.0006	0.9998
HKYIG	41	-4092.7417	8267.4833	0.0002	1.0000
GTRI	44	-4097.2907	8282.5814	0.0000	1.0000
HKYI	40	-4108.1858	8296.3715	0.0000	1.0000
GTR	43	-4176.7635	8439.5271	0.0000	1.0000
HKY	39	-4183.9280	8445.8560	0.0000	1.0000
SYMG	41	-4186.1085	8454.2171	0.0000	1.0000
SYMIG	42	-4186.1084	8456.2167	0.0000	1.0000
K2PG	37	-4193.4854	8460.9707	0.0000	1.0000
K2PIG	38	-4193.4853	8462.9705	0.0000	1.0000
F81G	39	-4193.3861	8464.7722	0.0000	1.0000
F81IG	40	-4198.5269	8477.0537	0.0000	1.0000
F81I	39	-4205.2653	8488.5305	0.0000	1.0000
SYMI	41	-4203.6069	8489.2137	0.0000	1.0000
K2PI	37	-4209.5939	8493.1879	0.0000	1.0000
JC69G	36	-4270.2711	8612.5422	0.0000	1.0000
JC69IG	37	-4274.8101	8623.6202	0.0000	1.0000
F81	38	-4280.0509	8636.1019	0.0000	1.0000
SYM	40	-4278.1577	8636.3154	0.0000	1.0000
JC69I	36	-4284.2268	8640.4536	0.0000	1.0000
K2P	36	-4287.0214	8646.0429	0.0000	1.0000
JC69	35	-4357.7865	8785.5730	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4092.7418	8455.8538	0.8847	0.8847
GTRG	44	-4081.5883	8460.5839	0.0831	0.9678
HKYIG	41	-4092.7417	8462.6128	0.0301	0.9980
GTRIG	45	-4081.9213	8468.0090	0.0020	1.0000
HKYI	40	-4108.1858	8486.7417	0.0000	1.0000
GTRI	44	-4097.2907	8491.9886	0.0000	1.0000
HKY	39	-4183.9280	8631.4670	0.0000	1.0000
K2PG	37	-4193.4854	8637.0632	0.0000	1.0000
K2PIG	38	-4193.4853	8643.8222	0.0000	1.0000
GTR	43	-4176.7635	8644.1750	0.0000	1.0000
SYMG	41	-4186.1085	8649.3466	0.0000	1.0000
F81G	39	-4193.3861	8650.3832	0.0000	1.0000
SYMIG	42	-4186.1084	8656.1054	0.0000	1.0000
F81IG	40	-4198.5269	8667.4240	0.0000	1.0000
K2PI	37	-4209.5939	8669.2803	0.0000	1.0000
F81I	39	-4205.2653	8674.1415	0.0000	1.0000
SYMI	41	-4203.6069	8684.3432	0.0000	1.0000
JC69G	36	-4270.2711	8783.8754	0.0000	1.0000
JC69IG	37	-4274.8101	8799.7126	0.0000	1.0000
JC69I	36	-4284.2268	8811.7868	0.0000	1.0000
F81	38	-4280.0509	8816.9536	0.0000	1.0000
K2P	36	-4287.0214	8817.3760	0.0000	1.0000
SYM	40	-4278.1577	8826.6856	0.0000	1.0000
JC69	35	-4357.7865	8952.1470	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/chr1_5492.phylip = 1 - 862;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5492.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/chr1_5492.phylip = 1 - 862;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5492.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/chr1_5492.phylip = 1 - 862;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5492.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

