
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:58 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_27317.phylip" (19 taxa, 252 characters)

Minimum AIC  model: HKY
Minimum AICc model: HKY
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
HKY	39	-539.2570	1171.2309	0.3753	0.3753
K2P	36	-544.2879	1172.9665	0.1576	0.5329
HKYI	40	-538.9207	1173.3864	0.1277	0.6606
HKYG	40	-538.9572	1173.4593	0.1232	0.7838
K2PI	37	-543.9713	1175.0828	0.0547	0.8385
K2PG	37	-544.0173	1175.1747	0.0522	0.8907
GTR	43	-535.9341	1176.0605	0.0335	0.9243
HKYIG	41	-538.9202	1176.2403	0.0307	0.9550
K2PIG	38	-543.9731	1177.8618	0.0136	0.9686
GTRI	44	-535.5671	1178.2646	0.0111	0.9797
GTRG	44	-535.6483	1178.4271	0.0103	0.9900
SYM	40	-542.3103	1180.1656	0.0043	0.9943
GTRIG	45	-535.5683	1181.2337	0.0025	0.9968
SYMI	41	-541.9672	1182.3345	0.0015	0.9983
SYMG	41	-542.0353	1182.4706	0.0014	0.9997
SYMIG	42	-541.9676	1185.2175	0.0003	1.0000
F81	38	-553.3239	1196.5633	0.0000	1.0000
F81I	39	-553.0188	1198.7546	0.0000	1.0000
F81G	39	-553.0559	1198.8289	0.0000	1.0000
JC69	35	-559.2326	1200.1318	0.0000	1.0000
F81IG	40	-553.0463	1201.6375	0.0000	1.0000
JC69I	36	-558.9205	1202.2316	0.0000	1.0000
JC69G	36	-558.9570	1202.3047	0.0000	1.0000
JC69IG	37	-558.9201	1204.9805	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKY	39	-539.2570	1156.5139	0.2740	0.2740
HKYI	40	-538.9207	1157.8414	0.1411	0.4151
GTR	43	-535.9341	1157.8682	0.1392	0.5543
HKYG	40	-538.9572	1157.9143	0.1360	0.6903
GTRI	44	-535.5671	1159.1342	0.0739	0.7642
GTRG	44	-535.6483	1159.2966	0.0682	0.8324
HKYIG	41	-538.9202	1159.8403	0.0519	0.8843
K2P	36	-544.2879	1160.5758	0.0359	0.9203
GTRIG	45	-535.5683	1161.1366	0.0272	0.9474
K2PI	37	-543.9713	1161.9426	0.0182	0.9656
K2PG	37	-544.0173	1162.0345	0.0173	0.9829
K2PIG	38	-543.9731	1163.9463	0.0067	0.9896
SYM	40	-542.3103	1164.6206	0.0048	0.9943
SYMI	41	-541.9672	1165.9345	0.0025	0.9968
SYMG	41	-542.0353	1166.0706	0.0023	0.9991
SYMIG	42	-541.9676	1167.9352	0.0009	1.0000
F81	38	-553.3239	1182.6478	0.0000	1.0000
F81I	39	-553.0188	1184.0376	0.0000	1.0000
F81G	39	-553.0559	1184.1119	0.0000	1.0000
F81IG	40	-553.0463	1186.0925	0.0000	1.0000
JC69	35	-559.2326	1188.4652	0.0000	1.0000
JC69I	36	-558.9205	1189.8409	0.0000	1.0000
JC69G	36	-558.9570	1189.9140	0.0000	1.0000
JC69IG	37	-558.9201	1191.8403	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-544.2879	1287.6353	0.8198	0.8198
K2PI	37	-543.9713	1292.5315	0.0709	0.8907
K2PG	37	-544.0173	1292.6234	0.0677	0.9584
HKY	39	-539.2570	1294.1617	0.0314	0.9898
K2PIG	38	-543.9731	1298.0646	0.0045	0.9943
HKYI	40	-538.9207	1299.0185	0.0028	0.9970
HKYG	40	-538.9572	1299.0915	0.0027	0.9997
HKYIG	41	-538.9202	1304.5469	0.0002	0.9999
SYM	40	-542.3103	1305.7977	0.0001	1.0000
GTR	43	-535.9341	1309.6337	0.0000	1.0000
SYMI	41	-541.9672	1310.6411	0.0000	1.0000
SYMG	41	-542.0353	1310.7772	0.0000	1.0000
JC69	35	-559.2326	1311.9952	0.0000	1.0000
GTRI	44	-535.5671	1314.4290	0.0000	1.0000
GTRG	44	-535.6483	1314.5915	0.0000	1.0000
SYMIG	42	-541.9676	1316.1712	0.0000	1.0000
F81	38	-553.3239	1316.7661	0.0000	1.0000
JC69I	36	-558.9205	1316.9004	0.0000	1.0000
JC69G	36	-558.9570	1316.9735	0.0000	1.0000
GTRIG	45	-535.5683	1319.9609	0.0000	1.0000
F81I	39	-553.0188	1321.6853	0.0000	1.0000
F81G	39	-553.0559	1321.7596	0.0000	1.0000
JC69IG	37	-558.9201	1322.4292	0.0000	1.0000
F81IG	40	-553.0463	1327.2697	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27317.phylip = 1 - 252;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27317.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27317.phylip = 1 - 252;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27317.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) 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_27317.phylip = 1 - 252;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_27317.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

