
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:40 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/chr4_7282.phylip" (19 taxa, 906 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	-3987.8455	8070.5049	0.9926	0.9926
GTRG	44	-3993.9934	8080.5861	0.0064	0.9990
HKYG	40	-4000.3668	8084.5254	0.0009	0.9999
HKYIG	41	-4001.7684	8089.5229	0.0001	1.0000
GTRI	44	-4006.4459	8105.4910	0.0000	1.0000
SYMG	41	-4011.3747	8108.7356	0.0000	1.0000
SYMIG	42	-4010.3891	8108.9636	0.0000	1.0000
HKYI	40	-4013.0581	8109.9080	0.0000	1.0000
K2PG	37	-4019.2184	8115.6763	0.0000	1.0000
K2PIG	38	-4018.1512	8115.7210	0.0000	1.0000
SYMI	41	-4024.3988	8134.7837	0.0000	1.0000
K2PI	37	-4029.4323	8136.1043	0.0000	1.0000
GTR	43	-4096.4612	8283.3123	0.0000	1.0000
HKY	39	-4101.2091	8284.0210	0.0000	1.0000
F81G	39	-4113.2842	8308.1712	0.0000	1.0000
F81IG	40	-4112.6901	8309.1721	0.0000	1.0000
SYM	40	-4116.0772	8315.9462	0.0000	1.0000
K2P	36	-4121.6420	8318.3496	0.0000	1.0000
JC69G	36	-4125.6003	8326.2663	0.0000	1.0000
JC69IG	37	-4124.9499	8327.1394	0.0000	1.0000
F81I	39	-4129.0505	8339.7039	0.0000	1.0000
JC69I	36	-4142.0237	8359.1130	0.0000	1.0000
F81	38	-4208.7907	8497.0001	0.0000	1.0000
JC69	35	-4225.8425	8524.5816	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRIG	45	-3987.8455	8065.6909	0.9936	0.9936
GTRG	44	-3993.9934	8075.9868	0.0058	0.9994
HKYG	40	-4000.3668	8080.7335	0.0005	1.0000
HKYIG	41	-4001.7684	8085.5367	0.0000	1.0000
GTRI	44	-4006.4459	8100.8917	0.0000	1.0000
SYMG	41	-4011.3747	8104.7495	0.0000	1.0000
SYMIG	42	-4010.3891	8104.7782	0.0000	1.0000
HKYI	40	-4013.0581	8106.1161	0.0000	1.0000
K2PIG	38	-4018.1512	8112.3023	0.0000	1.0000
K2PG	37	-4019.2184	8112.4367	0.0000	1.0000
SYMI	41	-4024.3988	8130.7976	0.0000	1.0000
K2PI	37	-4029.4323	8132.8647	0.0000	1.0000
GTR	43	-4096.4612	8278.9225	0.0000	1.0000
HKY	39	-4101.2091	8280.4182	0.0000	1.0000
F81G	39	-4113.2842	8304.5684	0.0000	1.0000
F81IG	40	-4112.6901	8305.3802	0.0000	1.0000
SYM	40	-4116.0772	8312.1543	0.0000	1.0000
K2P	36	-4121.6420	8315.2840	0.0000	1.0000
JC69G	36	-4125.6003	8323.2007	0.0000	1.0000
JC69IG	37	-4124.9499	8323.8997	0.0000	1.0000
F81I	39	-4129.0505	8336.1011	0.0000	1.0000
JC69I	36	-4142.0237	8356.0474	0.0000	1.0000
F81	38	-4208.7907	8493.5814	0.0000	1.0000
JC69	35	-4225.8425	8521.6850	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-4000.3668	8273.0951	0.9802	0.9802
GTRIG	45	-3987.8455	8282.0977	0.0109	0.9911
HKYIG	41	-4001.7684	8282.7074	0.0080	0.9991
GTRG	44	-3993.9934	8287.5846	0.0007	0.9998
K2PG	37	-4019.2184	8290.3712	0.0002	1.0000
K2PIG	38	-4018.1512	8295.0458	0.0000	1.0000
HKYI	40	-4013.0581	8298.4777	0.0000	1.0000
SYMG	41	-4011.3747	8301.9201	0.0000	1.0000
SYMIG	42	-4010.3891	8306.7579	0.0000	1.0000
K2PI	37	-4029.4323	8310.7991	0.0000	1.0000
GTRI	44	-4006.4459	8312.4894	0.0000	1.0000
SYMI	41	-4024.3988	8327.9682	0.0000	1.0000
HKY	39	-4101.2091	8467.9708	0.0000	1.0000
GTR	43	-4096.4612	8485.7112	0.0000	1.0000
K2P	36	-4121.6420	8488.4094	0.0000	1.0000
F81G	39	-4113.2842	8492.1209	0.0000	1.0000
JC69G	36	-4125.6003	8496.3261	0.0000	1.0000
F81IG	40	-4112.6901	8497.7418	0.0000	1.0000
JC69IG	37	-4124.9499	8501.8342	0.0000	1.0000
SYM	40	-4116.0772	8504.5159	0.0000	1.0000
F81I	39	-4129.0505	8523.6536	0.0000	1.0000
JC69I	36	-4142.0237	8529.1728	0.0000	1.0000
F81	38	-4208.7907	8676.3249	0.0000	1.0000
JC69	35	-4225.8425	8690.0014	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/chr4_7282.phylip = 1 - 906;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7282.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/chr4_7282.phylip = 1 - 906;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7282.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/chr4_7282.phylip = 1 - 906;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_7282.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;


-------------------------------------------------------------
End of Output

