
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:15 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/chr2_9170.phylip" (19 taxa, 954 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
Minimum BIC  model: K2PG


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	-4010.4681	8113.2927	0.4775	0.4775
GTRIG	45	-4010.3630	8115.2854	0.1763	0.6538
HKYG	40	-4016.0958	8115.7842	0.1374	0.7912
SYMG	41	-4015.0906	8115.9575	0.1260	0.9171
SYMIG	42	-4014.9006	8117.7660	0.0510	0.9681
HKYIG	41	-4016.4989	8118.7741	0.0308	0.9990
K2PG	37	-4024.4777	8126.0252	0.0008	0.9998
K2PIG	38	-4024.7772	8128.7937	0.0002	1.0000
GTRI	44	-4021.2685	8134.8934	0.0000	1.0000
HKYI	40	-4026.5638	8136.7201	0.0000	1.0000
SYMI	41	-4025.8646	8137.5055	0.0000	1.0000
K2PI	37	-4034.7384	8146.5466	0.0000	1.0000
F81IG	40	-4074.5291	8232.6507	0.0000	1.0000
F81G	39	-4075.9238	8233.2611	0.0000	1.0000
JC69IG	37	-4081.9868	8241.0435	0.0000	1.0000
JC69G	36	-4083.8100	8242.5251	0.0000	1.0000
F81I	39	-4086.1304	8253.6743	0.0000	1.0000
JC69I	36	-4093.8255	8262.5560	0.0000	1.0000
HKY	39	-4135.7607	8352.9350	0.0000	1.0000
GTR	43	-4133.0414	8356.2410	0.0000	1.0000
SYM	40	-4137.9218	8359.4361	0.0000	1.0000
K2P	36	-4144.1566	8363.2183	0.0000	1.0000
F81	38	-4190.3571	8459.9536	0.0000	1.0000
JC69	35	-4197.3720	8467.4892	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4010.4681	8108.9362	0.5155	0.5155
GTRIG	45	-4010.3630	8110.7259	0.2107	0.7262
SYMG	41	-4015.0906	8112.1812	0.1018	0.8280
HKYG	40	-4016.0958	8112.1916	0.1012	0.9292
SYMIG	42	-4014.9006	8113.8011	0.0453	0.9745
HKYIG	41	-4016.4989	8114.9977	0.0249	0.9994
K2PG	37	-4024.4777	8122.9554	0.0005	0.9999
K2PIG	38	-4024.7772	8125.5543	0.0001	1.0000
GTRI	44	-4021.2685	8130.5369	0.0000	1.0000
HKYI	40	-4026.5638	8133.1276	0.0000	1.0000
SYMI	41	-4025.8646	8133.7292	0.0000	1.0000
K2PI	37	-4034.7384	8143.4767	0.0000	1.0000
F81IG	40	-4074.5291	8229.0581	0.0000	1.0000
F81G	39	-4075.9238	8229.8476	0.0000	1.0000
JC69IG	37	-4081.9868	8237.9736	0.0000	1.0000
JC69G	36	-4083.8100	8239.6200	0.0000	1.0000
F81I	39	-4086.1304	8250.2607	0.0000	1.0000
JC69I	36	-4093.8255	8259.6509	0.0000	1.0000
HKY	39	-4135.7607	8349.5214	0.0000	1.0000
GTR	43	-4133.0414	8352.0827	0.0000	1.0000
SYM	40	-4137.9218	8355.8436	0.0000	1.0000
K2P	36	-4144.1566	8360.3132	0.0000	1.0000
F81	38	-4190.3571	8456.7143	0.0000	1.0000
JC69	35	-4197.3720	8464.7441	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-4024.4777	8302.7999	0.8410	0.8410
HKYG	40	-4016.0958	8306.6181	0.1246	0.9656
K2PIG	38	-4024.7772	8310.2595	0.0202	0.9858
SYMG	41	-4015.0906	8311.4684	0.0110	0.9968
HKYIG	41	-4016.4989	8314.2850	0.0027	0.9995
SYMIG	42	-4014.9006	8317.9490	0.0004	0.9999
GTRG	44	-4010.4681	8322.8054	0.0000	1.0000
K2PI	37	-4034.7384	8323.3213	0.0000	1.0000
HKYI	40	-4026.5638	8327.5541	0.0000	1.0000
GTRIG	45	-4010.3630	8329.4558	0.0000	1.0000
SYMI	41	-4025.8646	8333.0164	0.0000	1.0000
GTRI	44	-4021.2685	8344.4061	0.0000	1.0000
JC69G	36	-4083.8100	8414.6039	0.0000	1.0000
JC69IG	37	-4081.9868	8417.8182	0.0000	1.0000
F81G	39	-4075.9238	8419.4135	0.0000	1.0000
F81IG	40	-4074.5291	8423.4847	0.0000	1.0000
JC69I	36	-4093.8255	8434.6348	0.0000	1.0000
F81I	39	-4086.1304	8439.8266	0.0000	1.0000
K2P	36	-4144.1566	8535.2971	0.0000	1.0000
HKY	39	-4135.7607	8539.0873	0.0000	1.0000
SYM	40	-4137.9218	8550.2701	0.0000	1.0000
GTR	43	-4133.0414	8561.0913	0.0000	1.0000
JC69	35	-4197.3720	8634.8673	0.0000	1.0000
F81	38	-4190.3571	8641.4195	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/chr2_9170.phylip = 1 - 954;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_9170.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/chr2_9170.phylip = 1 - 954;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_9170.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 (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_9170.phylip = 1 - 954;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_9170.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

