
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:10 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/chr8_4048.phylip" (19 taxa, 1074 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	-4153.7361	8399.3205	0.6240	0.6240
GTRIG	45	-4153.1557	8400.3386	0.3751	0.9991
HKYG	40	-4165.0772	8413.3297	0.0006	0.9997
HKYIG	41	-4164.5268	8414.3908	0.0003	1.0000
GTRI	44	-4168.7553	8429.3589	0.0000	1.0000
HKYI	40	-4176.0353	8435.2458	0.0000	1.0000
SYMIG	42	-4176.6796	8440.8626	0.0000	1.0000
K2PG	37	-4183.3250	8443.3643	0.0000	1.0000
K2PIG	38	-4182.7227	8444.3093	0.0000	1.0000
SYMG	41	-4180.0581	8445.4534	0.0000	1.0000
K2PI	37	-4194.1456	8465.0055	0.0000	1.0000
SYMI	41	-4191.1490	8467.6352	0.0000	1.0000
F81IG	40	-4234.8528	8552.8807	0.0000	1.0000
JC69G	36	-4246.8877	8568.3443	0.0000	1.0000
F81G	39	-4245.8810	8572.7795	0.0000	1.0000
JC69IG	37	-4248.8126	8574.3395	0.0000	1.0000
F81I	39	-4255.2359	8591.4891	0.0000	1.0000
JC69I	36	-4268.9108	8612.3906	0.0000	1.0000
GTR	43	-4284.3052	8658.2841	0.0000	1.0000
HKY	39	-4292.2819	8665.5813	0.0000	1.0000
K2P	36	-4310.4409	8695.4507	0.0000	1.0000
SYM	40	-4307.4648	8698.1049	0.0000	1.0000
F81	38	-4360.3163	8799.4964	0.0000	1.0000
JC69	35	-4374.4450	8821.3176	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-4153.7361	8395.4721	0.6030	0.6030
GTRIG	45	-4153.1557	8396.3114	0.3964	0.9994
HKYG	40	-4165.0772	8410.1545	0.0004	0.9998
HKYIG	41	-4164.5268	8411.0536	0.0002	1.0000
GTRI	44	-4168.7553	8425.5105	0.0000	1.0000
HKYI	40	-4176.0353	8432.0706	0.0000	1.0000
SYMIG	42	-4176.6796	8437.3592	0.0000	1.0000
K2PG	37	-4183.3250	8440.6500	0.0000	1.0000
K2PIG	38	-4182.7227	8441.4455	0.0000	1.0000
SYMG	41	-4180.0581	8442.1162	0.0000	1.0000
K2PI	37	-4194.1456	8462.2912	0.0000	1.0000
SYMI	41	-4191.1490	8464.2980	0.0000	1.0000
F81IG	40	-4234.8528	8549.7055	0.0000	1.0000
JC69G	36	-4246.8877	8565.7754	0.0000	1.0000
F81G	39	-4245.8810	8569.7621	0.0000	1.0000
JC69IG	37	-4248.8126	8571.6252	0.0000	1.0000
F81I	39	-4255.2359	8588.4717	0.0000	1.0000
JC69I	36	-4268.9108	8609.8217	0.0000	1.0000
GTR	43	-4284.3052	8654.6103	0.0000	1.0000
HKY	39	-4292.2819	8662.5639	0.0000	1.0000
K2P	36	-4310.4409	8692.8818	0.0000	1.0000
SYM	40	-4307.4648	8694.9297	0.0000	1.0000
F81	38	-4360.3163	8796.6326	0.0000	1.0000
JC69	35	-4374.4450	8818.8899	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4165.0772	8609.3203	0.8847	0.8847
GTRG	44	-4153.7361	8614.5545	0.0646	0.9493
HKYIG	41	-4164.5268	8615.1985	0.0468	0.9961
GTRIG	45	-4153.1557	8620.3729	0.0035	0.9996
K2PG	37	-4183.3250	8624.8784	0.0004	1.0000
K2PIG	38	-4182.7227	8630.6530	0.0000	1.0000
HKYI	40	-4176.0353	8631.2364	0.0000	1.0000
GTRI	44	-4168.7553	8644.5929	0.0000	1.0000
SYMG	41	-4180.0581	8646.2611	0.0000	1.0000
SYMIG	42	-4176.6796	8646.4833	0.0000	1.0000
K2PI	37	-4194.1456	8646.5196	0.0000	1.0000
SYMI	41	-4191.1490	8668.4430	0.0000	1.0000
JC69G	36	-4246.8877	8745.0246	0.0000	1.0000
F81IG	40	-4234.8528	8748.8713	0.0000	1.0000
JC69IG	37	-4248.8126	8755.8536	0.0000	1.0000
F81G	39	-4245.8810	8763.9487	0.0000	1.0000
F81I	39	-4255.2359	8782.6584	0.0000	1.0000
JC69I	36	-4268.9108	8789.0709	0.0000	1.0000
HKY	39	-4292.2819	8856.7505	0.0000	1.0000
GTR	43	-4284.3052	8868.7136	0.0000	1.0000
K2P	36	-4310.4409	8872.1310	0.0000	1.0000
SYM	40	-4307.4648	8894.0955	0.0000	1.0000
F81	38	-4360.3163	8985.8401	0.0000	1.0000
JC69	35	-4374.4450	8993.1600	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/chr8_4048.phylip = 1 - 1074;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4048.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/chr8_4048.phylip = 1 - 1074;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4048.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/chr8_4048.phylip = 1 - 1074;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_4048.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

