
Output from mraic.pl version 1.4.4 by Johan Nylander
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13:19 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/chrZ_4819.phylip" (19 taxa, 584 characters)

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


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	-1419.9438	2935.2346	0.5448	0.5448
GTRI	44	-1420.6269	2936.6007	0.2752	0.8200
GTRIG	45	-1419.9301	2937.5554	0.1707	0.9907
GTR	43	-1425.1869	2943.3813	0.0093	1.0000
HKYG	40	-1444.7179	2975.4763	0.0000	1.0000
HKYI	40	-1445.1622	2976.3648	0.0000	1.0000
HKYIG	41	-1444.6973	2977.7488	0.0000	1.0000
SYMG	41	-1445.4742	2979.3027	0.0000	1.0000
SYMI	41	-1446.0216	2980.3974	0.0000	1.0000
SYMIG	42	-1445.4642	2981.6050	0.0000	1.0000
HKY	39	-1450.1402	2984.0158	0.0000	1.0000
SYM	40	-1450.4006	2986.8418	0.0000	1.0000
K2PG	37	-1462.0769	3003.3039	0.0000	1.0000
K2PI	37	-1462.5060	3004.1623	0.0000	1.0000
K2PIG	38	-1462.0467	3005.5320	0.0000	1.0000
K2P	36	-1467.9869	3012.8441	0.0000	1.0000
F81G	39	-1466.1040	3015.9434	0.0000	1.0000
F81I	39	-1466.6286	3016.9925	0.0000	1.0000
F81IG	40	-1466.0835	3018.2074	0.0000	1.0000
F81	38	-1471.2544	3023.9474	0.0000	1.0000
JC69G	36	-1480.9948	3038.8599	0.0000	1.0000
JC69I	36	-1481.5102	3039.8906	0.0000	1.0000
JC69IG	37	-1480.9670	3041.0843	0.0000	1.0000
JC69	35	-1486.4382	3047.4750	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1419.9438	2927.8876	0.5284	0.5284
GTRI	44	-1420.6269	2929.2537	0.2669	0.7953
GTRIG	45	-1419.9301	2929.8603	0.1971	0.9924
GTR	43	-1425.1869	2936.3739	0.0076	1.0000
HKYG	40	-1444.7179	2969.4358	0.0000	1.0000
HKYI	40	-1445.1622	2970.3243	0.0000	1.0000
HKYIG	41	-1444.6973	2971.3946	0.0000	1.0000
SYMG	41	-1445.4742	2972.9484	0.0000	1.0000
SYMI	41	-1446.0216	2974.0432	0.0000	1.0000
SYMIG	42	-1445.4642	2974.9285	0.0000	1.0000
HKY	39	-1450.1402	2978.2805	0.0000	1.0000
SYM	40	-1450.4006	2980.8013	0.0000	1.0000
K2PG	37	-1462.0769	2998.1538	0.0000	1.0000
K2PI	37	-1462.5060	2999.0121	0.0000	1.0000
K2PIG	38	-1462.0467	3000.0935	0.0000	1.0000
K2P	36	-1467.9869	3007.9739	0.0000	1.0000
F81G	39	-1466.1040	3010.2081	0.0000	1.0000
F81I	39	-1466.6286	3011.2572	0.0000	1.0000
F81IG	40	-1466.0835	3012.1669	0.0000	1.0000
F81	38	-1471.2544	3018.5089	0.0000	1.0000
JC69G	36	-1480.9948	3033.9897	0.0000	1.0000
JC69I	36	-1481.5102	3035.0204	0.0000	1.0000
JC69IG	37	-1480.9670	3035.9341	0.0000	1.0000
JC69	35	-1486.4382	3042.8764	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
GTRG	44	-1419.9438	3120.1633	0.5971	0.5971
GTRI	44	-1420.6269	3121.5294	0.3016	0.8987
GTR	43	-1425.1869	3124.2796	0.0762	0.9749
GTRIG	45	-1419.9301	3126.5058	0.0250	1.0000
HKYG	40	-1444.7179	3144.2318	0.0000	1.0000
HKYI	40	-1445.1622	3145.1204	0.0000	1.0000
HKY	39	-1450.1402	3148.7066	0.0000	1.0000
HKYIG	41	-1444.6973	3150.5605	0.0000	1.0000
SYMG	41	-1445.4742	3152.1144	0.0000	1.0000
SYMI	41	-1446.0216	3153.2091	0.0000	1.0000
SYM	40	-1450.4006	3155.5973	0.0000	1.0000
SYMIG	42	-1445.4642	3158.4643	0.0000	1.0000
K2PG	37	-1462.0769	3159.8401	0.0000	1.0000
K2PI	37	-1462.5060	3160.6984	0.0000	1.0000
K2P	36	-1467.9869	3165.2903	0.0000	1.0000
K2PIG	38	-1462.0467	3166.1497	0.0000	1.0000
F81G	39	-1466.1040	3180.6342	0.0000	1.0000
F81I	39	-1466.6286	3181.6833	0.0000	1.0000
F81	38	-1471.2544	3184.5651	0.0000	1.0000
F81IG	40	-1466.0835	3186.9630	0.0000	1.0000
JC69G	36	-1480.9948	3191.3061	0.0000	1.0000
JC69I	36	-1481.5102	3192.3368	0.0000	1.0000
JC69	35	-1486.4382	3195.8230	0.0000	1.0000
JC69IG	37	-1480.9670	3197.6204	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/chrZ_4819.phylip = 1 - 584;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4819.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/chrZ_4819.phylip = 1 - 584;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4819.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4819.phylip = 1 - 584;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chrZ_4819.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;


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End of Output

