
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:36 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/chr6_3274.phylip" (19 taxa, 376 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: K2PG


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
HKYG	40	-1459.1664	3008.1238	0.6517	0.6517
HKYIG	41	-1458.8117	3009.9347	0.2635	0.9153
HKYI	40	-1462.4198	3014.6306	0.0252	0.9404
K2PG	37	-1466.2731	3014.8658	0.0224	0.9628
GTRG	44	-1457.6183	3015.2003	0.0189	0.9818
K2PIG	38	-1465.9451	3016.6855	0.0090	0.9908
GTRIG	45	-1457.3115	3017.1684	0.0071	0.9979
K2PI	37	-1469.1927	3020.7049	0.0012	0.9991
GTRI	44	-1461.0507	3022.0651	0.0006	0.9997
SYMG	41	-1465.9206	3024.1525	0.0002	0.9999
SYMIG	42	-1465.5954	3026.0376	0.0001	1.0000
SYMI	41	-1468.8562	3030.0237	0.0000	1.0000
HKY	39	-1492.3763	3072.0383	0.0000	1.0000
K2P	36	-1498.9228	3077.7040	0.0000	1.0000
GTR	43	-1491.1245	3079.6467	0.0000	1.0000
F81G	39	-1499.2666	3085.8188	0.0000	1.0000
SYM	40	-1498.6501	3087.0912	0.0000	1.0000
F81IG	40	-1499.0864	3087.9639	0.0000	1.0000
F81I	39	-1501.9491	3091.1839	0.0000	1.0000
JC69G	36	-1506.3249	3092.5082	0.0000	1.0000
JC69IG	37	-1506.1368	3094.5931	0.0000	1.0000
JC69I	36	-1508.8918	3097.6421	0.0000	1.0000
F81	38	-1530.6493	3146.0940	0.0000	1.0000
JC69	35	-1537.4576	3152.3270	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1459.1664	2998.3328	0.5809	0.5809
HKYIG	41	-1458.8117	2999.6233	0.3047	0.8855
GTRG	44	-1457.6183	3003.2366	0.0500	0.9356
GTRIG	45	-1457.3115	3004.6230	0.0250	0.9606
HKYI	40	-1462.4198	3004.8395	0.0224	0.9830
K2PG	37	-1466.2731	3006.5463	0.0096	0.9926
K2PIG	38	-1465.9451	3007.8902	0.0049	0.9975
GTRI	44	-1461.0507	3010.1013	0.0016	0.9991
K2PI	37	-1469.1927	3012.3854	0.0005	0.9996
SYMG	41	-1465.9206	3013.8411	0.0002	0.9999
SYMIG	42	-1465.5954	3015.1908	0.0001	1.0000
SYMI	41	-1468.8562	3019.7123	0.0000	1.0000
HKY	39	-1492.3763	3062.7525	0.0000	1.0000
GTR	43	-1491.1245	3068.2491	0.0000	1.0000
K2P	36	-1498.9228	3069.8456	0.0000	1.0000
F81G	39	-1499.2666	3076.5331	0.0000	1.0000
SYM	40	-1498.6501	3077.3002	0.0000	1.0000
F81IG	40	-1499.0864	3078.1728	0.0000	1.0000
F81I	39	-1501.9491	3081.8982	0.0000	1.0000
JC69G	36	-1506.3249	3084.6498	0.0000	1.0000
JC69IG	37	-1506.1368	3086.2736	0.0000	1.0000
JC69I	36	-1508.8918	3089.7837	0.0000	1.0000
F81	38	-1530.6493	3137.2987	0.0000	1.0000
JC69	35	-1537.4576	3144.9152	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1466.2731	3151.9411	0.7624	0.7624
HKYG	40	-1459.1664	3155.5163	0.1276	0.8900
K2PIG	38	-1465.9451	3157.2146	0.0546	0.9445
K2PI	37	-1469.1927	3157.7802	0.0411	0.9857
HKYIG	41	-1458.8117	3160.7365	0.0094	0.9951
HKYI	40	-1462.4198	3162.0231	0.0049	1.0000
SYMG	41	-1465.9206	3174.9543	0.0000	1.0000
GTRG	44	-1457.6183	3176.1385	0.0000	1.0000
SYMIG	42	-1465.5954	3180.2335	0.0000	1.0000
SYMI	41	-1468.8562	3180.8255	0.0000	1.0000
GTRIG	45	-1457.3115	3181.4545	0.0000	1.0000
GTRI	44	-1461.0507	3183.0032	0.0000	1.0000
K2P	36	-1498.9228	3211.3108	0.0000	1.0000
HKY	39	-1492.3763	3216.0065	0.0000	1.0000
JC69G	36	-1506.3249	3226.1150	0.0000	1.0000
F81G	39	-1499.2666	3229.7871	0.0000	1.0000
JC69I	36	-1508.8918	3231.2489	0.0000	1.0000
JC69IG	37	-1506.1368	3231.6684	0.0000	1.0000
SYM	40	-1498.6501	3234.4838	0.0000	1.0000
F81I	39	-1501.9491	3235.1522	0.0000	1.0000
F81IG	40	-1499.0864	3235.3564	0.0000	1.0000
GTR	43	-1491.1245	3237.2214	0.0000	1.0000
JC69	35	-1537.4576	3282.4509	0.0000	1.0000
F81	38	-1530.6493	3286.6231	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3274.phylip = 1 - 376;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3274.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3274.phylip = 1 - 376;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3274.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;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3274.phylip = 1 - 376;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr6_3274.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

