
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:25 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_9603.phylip" (19 taxa, 646 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-3031.2824	6150.2668	0.4562	0.4562
HKYG	40	-3033.1074	6151.6362	0.2300	0.6862
GTRIG	45	-3027.6558	6152.2116	0.1725	0.8588
GTRG	44	-3029.0162	6152.6214	0.1406	0.9993
HKYI	40	-3039.0392	6163.5000	0.0006	0.9999
K2PIG	38	-3044.3840	6169.6510	0.0000	1.0000
K2PG	37	-3046.0183	6170.6615	0.0000	1.0000
GTRI	44	-3038.6809	6171.9507	0.0000	1.0000
SYMIG	42	-3043.6502	6177.2905	0.0000	1.0000
SYMG	41	-3045.2942	6178.2904	0.0000	1.0000
K2PI	37	-3050.8842	6180.3934	0.0000	1.0000
SYMI	41	-3051.1042	6189.9104	0.0000	1.0000
F81IG	40	-3146.6926	6378.8067	0.0000	1.0000
F81G	39	-3148.4371	6380.0227	0.0000	1.0000
F81I	39	-3151.0830	6385.3145	0.0000	1.0000
JC69IG	37	-3153.9379	6386.5009	0.0000	1.0000
JC69G	36	-3156.1140	6388.6024	0.0000	1.0000
HKY	39	-3153.2994	6389.7474	0.0000	1.0000
JC69I	36	-3157.8767	6392.1278	0.0000	1.0000
GTR	43	-3150.9236	6394.1330	0.0000	1.0000
K2P	36	-3162.4444	6401.2633	0.0000	1.0000
SYM	40	-3160.3162	6406.0539	0.0000	1.0000
F81	38	-3254.2021	6589.2872	0.0000	1.0000
JC69	35	-3260.4753	6595.0818	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-3031.2824	6144.5648	0.3834	0.3834
GTRIG	45	-3027.6558	6145.3116	0.2640	0.6474
GTRG	44	-3029.0162	6146.0324	0.1841	0.8315
HKYG	40	-3033.1074	6146.2148	0.1680	0.9995
HKYI	40	-3039.0392	6158.0785	0.0004	1.0000
K2PIG	38	-3044.3840	6164.7680	0.0000	1.0000
GTRI	44	-3038.6809	6165.3617	0.0000	1.0000
K2PG	37	-3046.0183	6166.0365	0.0000	1.0000
SYMIG	42	-3043.6502	6171.3004	0.0000	1.0000
SYMG	41	-3045.2942	6172.5884	0.0000	1.0000
K2PI	37	-3050.8842	6175.7684	0.0000	1.0000
SYMI	41	-3051.1042	6184.2084	0.0000	1.0000
F81IG	40	-3146.6926	6373.3853	0.0000	1.0000
F81G	39	-3148.4371	6374.8742	0.0000	1.0000
F81I	39	-3151.0830	6380.1659	0.0000	1.0000
JC69IG	37	-3153.9379	6381.8759	0.0000	1.0000
JC69G	36	-3156.1140	6384.2280	0.0000	1.0000
HKY	39	-3153.2994	6384.5989	0.0000	1.0000
JC69I	36	-3157.8767	6387.7534	0.0000	1.0000
GTR	43	-3150.9236	6387.8473	0.0000	1.0000
K2P	36	-3162.4444	6396.8889	0.0000	1.0000
SYM	40	-3160.3162	6400.6325	0.0000	1.0000
F81	38	-3254.2021	6584.4041	0.0000	1.0000
JC69	35	-3260.4753	6590.9507	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-3033.1074	6325.0467	0.7717	0.7717
HKYIG	41	-3031.2824	6327.8676	0.1883	0.9600
K2PG	37	-3046.0183	6331.4561	0.0313	0.9913
K2PIG	38	-3044.3840	6334.6584	0.0063	0.9976
HKYI	40	-3039.0392	6336.9105	0.0020	0.9996
K2PI	37	-3050.8842	6341.1880	0.0002	0.9999
GTRG	44	-3029.0162	6342.7476	0.0001	1.0000
GTRIG	45	-3027.6558	6346.4976	0.0000	1.0000
SYMG	41	-3045.2942	6355.8912	0.0000	1.0000
SYMIG	42	-3043.6502	6359.0740	0.0000	1.0000
GTRI	44	-3038.6809	6362.0769	0.0000	1.0000
SYMI	41	-3051.1042	6367.5112	0.0000	1.0000
JC69G	36	-3156.1140	6545.1768	0.0000	1.0000
JC69IG	37	-3153.9379	6547.2955	0.0000	1.0000
JC69I	36	-3157.8767	6548.7022	0.0000	1.0000
F81G	39	-3148.4371	6549.2354	0.0000	1.0000
F81IG	40	-3146.6926	6552.2172	0.0000	1.0000
F81I	39	-3151.0830	6554.5271	0.0000	1.0000
K2P	36	-3162.4444	6557.8377	0.0000	1.0000
HKY	39	-3153.2994	6558.9600	0.0000	1.0000
SYM	40	-3160.3162	6579.4644	0.0000	1.0000
GTR	43	-3150.9236	6580.0916	0.0000	1.0000
JC69	35	-3260.4753	6747.4286	0.0000	1.0000
F81	38	-3254.2021	6754.2945	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9603.phylip = 1 - 646;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9603.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best AICc model (HKYIG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9603.phylip = 1 - 646;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9603.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 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) 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_9603.phylip = 1 - 646;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9603.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

