
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:11 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/chr2_8688.phylip" (19 taxa, 225 characters)

Minimum AIC  model: SYM
Minimum AICc model: K2P
Minimum BIC  model: K2P


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
K2P	36	-517.3576	1120.8855	0.2850	0.2850
K2PG	37	-516.2944	1121.6263	0.1968	0.4817
K2PI	37	-516.4511	1121.9397	0.1682	0.6500
SYM	40	-512.3369	1122.4999	0.1271	0.7771
SYMI	41	-511.6183	1124.0564	0.0584	0.8355
SYMG	41	-511.8086	1124.4368	0.0483	0.8837
K2PIG	38	-516.2942	1124.5239	0.0462	0.9299
HKY	39	-515.7092	1126.2833	0.0192	0.9491
SYMIG	42	-511.6655	1127.1772	0.0123	0.9614
HKYG	40	-514.6767	1127.1795	0.0122	0.9736
HKYI	40	-514.8370	1127.5000	0.0104	0.9841
GTR	43	-510.8662	1128.6385	0.0059	0.9900
GTRI	44	-509.8902	1129.7804	0.0033	0.9933
GTRG	44	-509.9310	1129.8620	0.0032	0.9965
HKYIG	41	-514.6774	1130.1744	0.0027	0.9992
GTRIG	45	-509.8907	1132.9099	0.0007	0.9999
JC69	35	-528.1274	1139.5881	0.0000	1.0000
JC69I	36	-527.3579	1140.8860	0.0000	1.0000
JC69G	36	-527.4411	1141.0525	0.0000	1.0000
JC69IG	37	-527.3611	1143.7596	0.0000	1.0000
F81	38	-526.5412	1145.0178	0.0000	1.0000
F81I	39	-525.7688	1146.4025	0.0000	1.0000
F81G	39	-525.8543	1146.5735	0.0000	1.0000
F81IG	40	-525.7718	1149.3697	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYM	40	-512.3369	1104.6738	0.2052	0.2052
SYMI	41	-511.6183	1105.2367	0.1549	0.3601
SYMG	41	-511.8086	1105.6171	0.1280	0.4881
K2PG	37	-516.2944	1106.5888	0.0788	0.5669
K2P	36	-517.3576	1106.7152	0.0739	0.6408
K2PI	37	-516.4511	1106.9022	0.0673	0.7081
SYMIG	42	-511.6655	1107.3310	0.0543	0.7625
GTR	43	-510.8662	1107.7324	0.0445	0.8069
GTRI	44	-509.8902	1107.7804	0.0434	0.8503
GTRG	44	-509.9310	1107.8620	0.0417	0.8920
K2PIG	38	-516.2942	1108.5884	0.0290	0.9210
HKYG	40	-514.6767	1109.3534	0.0198	0.9408
HKY	39	-515.7092	1109.4184	0.0191	0.9599
HKYI	40	-514.8370	1109.6739	0.0168	0.9768
GTRIG	45	-509.8907	1109.7814	0.0160	0.9927
HKYIG	41	-514.6774	1111.3547	0.0073	1.0000
JC69	35	-528.1274	1126.2547	0.0000	1.0000
JC69I	36	-527.3579	1126.7158	0.0000	1.0000
JC69G	36	-527.4411	1126.8822	0.0000	1.0000
JC69IG	37	-527.3611	1128.7222	0.0000	1.0000
F81	38	-526.5412	1129.0824	0.0000	1.0000
F81I	39	-525.7688	1129.5376	0.0000	1.0000
F81G	39	-525.8543	1129.7086	0.0000	1.0000
F81IG	40	-525.7718	1131.5436	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-517.3576	1229.6949	0.7261	0.7261
K2PG	37	-516.2944	1232.9845	0.1402	0.8663
K2PI	37	-516.4511	1233.2979	0.1198	0.9861
K2PIG	38	-516.2942	1238.4002	0.0093	0.9954
SYM	40	-512.3369	1241.3178	0.0022	0.9976
HKY	39	-515.7092	1242.6463	0.0011	0.9987
SYMI	41	-511.6183	1245.2968	0.0003	0.9990
SYMG	41	-511.8086	1245.6772	0.0002	0.9993
JC69	35	-528.1274	1245.8183	0.0002	0.9995
HKYG	40	-514.6767	1245.9974	0.0002	0.9997
HKYI	40	-514.8370	1246.3179	0.0002	0.9999
JC69I	36	-527.3579	1249.6954	0.0000	0.9999
JC69G	36	-527.4411	1249.8619	0.0000	1.0000
SYMIG	42	-511.6655	1250.8072	0.0000	1.0000
HKYIG	41	-514.6774	1251.4149	0.0000	1.0000
GTR	43	-510.8662	1254.6247	0.0000	1.0000
JC69IG	37	-527.3611	1255.1179	0.0000	1.0000
GTRI	44	-509.8902	1258.0889	0.0000	1.0000
GTRG	44	-509.9310	1258.1704	0.0000	1.0000
F81	38	-526.5412	1258.8942	0.0000	1.0000
F81I	39	-525.7688	1262.7655	0.0000	1.0000
F81G	39	-525.8543	1262.9365	0.0000	1.0000
GTRIG	45	-509.8907	1263.5059	0.0000	1.0000
F81IG	40	-525.7718	1268.1877	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8688.phylip = 1 - 225;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8688.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=equal;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Fixed(Equal);
END;


[Mrbayes block for the best AICc model (K2P)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8688.phylip = 1 - 225;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8688.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


[Mrbayes block for the best BIC model (K2P)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8688.phylip = 1 - 225;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_8688.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


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End of Output

