
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:15 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/chr8_7531.phylip" (19 taxa, 451 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	-1449.2556	2996.2650	0.3603	0.3603
HKYG	40	-1454.7257	2997.4514	0.1991	0.5594
GTRI	44	-1449.9137	2997.5812	0.1866	0.7460
GTRIG	45	-1449.1461	2998.5144	0.1170	0.8630
HKYI	40	-1455.6867	2999.3733	0.0762	0.9392
HKYIG	41	-1454.7018	2999.8242	0.0608	0.9999
GTR	43	-1459.5115	3014.3202	0.0000	1.0000
HKY	39	-1465.4518	3016.4949	0.0000	1.0000
K2PG	37	-1479.7807	3040.3702	0.0000	1.0000
F81G	39	-1477.7869	3041.1650	0.0000	1.0000
K2PI	37	-1480.9178	3042.6444	0.0000	1.0000
F81I	39	-1478.5575	3042.7063	0.0000	1.0000
K2PIG	38	-1479.7781	3042.7503	0.0000	1.0000
F81IG	40	-1477.7892	3043.5785	0.0000	1.0000
SYMG	41	-1478.4379	3047.2964	0.0000	1.0000
SYMI	41	-1479.4245	3049.2695	0.0000	1.0000
SYMIG	42	-1478.4327	3049.7184	0.0000	1.0000
F81	38	-1486.8359	3056.8660	0.0000	1.0000
K2P	36	-1490.0122	3058.4592	0.0000	1.0000
SYM	40	-1488.4910	3064.9820	0.0000	1.0000
JC69G	36	-1500.7493	3079.9334	0.0000	1.0000
JC69I	36	-1501.6884	3081.8116	0.0000	1.0000
JC69IG	37	-1500.7538	3082.3164	0.0000	1.0000
JC69	35	-1509.9305	3095.9332	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1449.2556	2986.5113	0.4287	0.4287
GTRI	44	-1449.9137	2987.8275	0.2220	0.6506
GTRIG	45	-1449.1461	2988.2922	0.1760	0.8266
HKYG	40	-1454.7257	2989.4514	0.0985	0.9251
HKYI	40	-1455.6867	2991.3733	0.0377	0.9628
HKYIG	41	-1454.7018	2991.4037	0.0371	1.0000
GTR	43	-1459.5115	3005.0229	0.0000	1.0000
HKY	39	-1465.4518	3008.9037	0.0000	1.0000
K2PG	37	-1479.7807	3033.5615	0.0000	1.0000
F81G	39	-1477.7869	3033.5737	0.0000	1.0000
F81I	39	-1478.5575	3035.1151	0.0000	1.0000
K2PIG	38	-1479.7781	3035.5562	0.0000	1.0000
F81IG	40	-1477.7892	3035.5785	0.0000	1.0000
K2PI	37	-1480.9178	3035.8357	0.0000	1.0000
SYMG	41	-1478.4379	3038.8759	0.0000	1.0000
SYMI	41	-1479.4245	3040.8490	0.0000	1.0000
SYMIG	42	-1478.4327	3040.8654	0.0000	1.0000
F81	38	-1486.8359	3049.6719	0.0000	1.0000
K2P	36	-1490.0122	3052.0245	0.0000	1.0000
SYM	40	-1488.4910	3056.9820	0.0000	1.0000
JC69G	36	-1500.7493	3073.4986	0.0000	1.0000
JC69I	36	-1501.6884	3075.3768	0.0000	1.0000
JC69IG	37	-1500.7538	3075.5076	0.0000	1.0000
JC69	35	-1509.9305	3089.8609	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1454.7257	3153.9101	0.6978	0.6978
HKYI	40	-1455.6867	3155.8320	0.2669	0.9647
HKYIG	41	-1454.7018	3159.9738	0.0337	0.9984
GTRG	44	-1449.2556	3167.4158	0.0008	0.9992
GTRI	44	-1449.9137	3168.7320	0.0004	0.9996
HKY	39	-1465.4518	3169.2509	0.0003	1.0000
GTRIG	45	-1449.1461	3173.3082	0.0000	1.0000
GTR	43	-1459.5115	3181.8160	0.0000	1.0000
K2PG	37	-1479.7807	3185.6858	0.0000	1.0000
K2PI	37	-1480.9178	3187.9600	0.0000	1.0000
K2PIG	38	-1479.7781	3191.7919	0.0000	1.0000
F81G	39	-1477.7869	3193.9209	0.0000	1.0000
F81I	39	-1478.5575	3195.4623	0.0000	1.0000
F81IG	40	-1477.7892	3200.0372	0.0000	1.0000
K2P	36	-1490.0122	3200.0373	0.0000	1.0000
F81	38	-1486.8359	3205.9076	0.0000	1.0000
SYMG	41	-1478.4379	3207.4460	0.0000	1.0000
SYMI	41	-1479.4245	3209.4192	0.0000	1.0000
SYMIG	42	-1478.4327	3213.5471	0.0000	1.0000
SYM	40	-1488.4910	3221.4407	0.0000	1.0000
JC69G	36	-1500.7493	3221.5114	0.0000	1.0000
JC69I	36	-1501.6884	3223.3897	0.0000	1.0000
JC69IG	37	-1500.7538	3227.6319	0.0000	1.0000
JC69	35	-1509.9305	3233.7623	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_7531.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_7531.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_7531.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_7531.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_7531.phylip = 1 - 451;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_7531.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

