
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:57 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/chr8_1565.phylip" (19 taxa, 209 characters)

Minimum AIC  model: GTRI
Minimum AICc model: SYMI
Minimum BIC  model: K2PI


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
SYMI	41	-536.2380	1175.0988	0.1535	0.1535
SYMG	41	-536.4408	1175.5044	0.1253	0.2789
K2PI	37	-542.5724	1175.5893	0.1201	0.3990
K2PG	37	-542.8028	1176.0501	0.0954	0.4944
GTRI	44	-532.2342	1176.6148	0.0719	0.5664
HKYI	40	-538.6152	1176.7542	0.0671	0.6335
GTRG	44	-532.4007	1176.9477	0.0609	0.6944
HKYG	40	-538.8321	1177.1880	0.0540	0.7484
SYM	40	-539.1089	1177.7417	0.0410	0.7894
SYMIG	42	-536.4590	1178.6771	0.0257	0.8150
JC69I	36	-545.6414	1178.7712	0.0245	0.8395
F81I	39	-541.2284	1178.9183	0.0227	0.8622
K2PIG	38	-542.8024	1179.0401	0.0214	0.8836
GTR	43	-535.1052	1179.1438	0.0203	0.9039
JC69G	36	-545.8519	1179.1922	0.0198	0.9238
F81G	39	-541.4186	1179.2987	0.0188	0.9426
K2P	36	-546.3061	1180.1005	0.0126	0.9552
GTRIG	45	-532.4171	1180.2330	0.0118	0.9670
HKYIG	41	-538.8317	1180.2862	0.0115	0.9784
HKY	39	-542.1955	1180.8526	0.0086	0.9871
JC69IG	37	-545.9072	1182.2588	0.0043	0.9914
F81IG	40	-541.4752	1182.4741	0.0038	0.9952
JC69	35	-549.3415	1183.2495	0.0026	0.9978
F81	38	-545.0812	1183.5977	0.0022	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-532.2342	1152.4685	0.2886	0.2886
GTRG	44	-532.4007	1152.8014	0.2444	0.5330
SYMI	41	-536.2380	1154.4760	0.1058	0.6388
GTRIG	45	-532.4171	1154.8342	0.0884	0.7272
SYMG	41	-536.4408	1154.8817	0.0864	0.8136
GTR	43	-535.1052	1156.2105	0.0444	0.8580
SYMIG	42	-536.4590	1156.9180	0.0312	0.8892
HKYI	40	-538.6152	1157.2304	0.0267	0.9159
HKYG	40	-538.8321	1157.6642	0.0215	0.9374
SYM	40	-539.1089	1158.2179	0.0163	0.9537
K2PI	37	-542.5724	1159.1449	0.0102	0.9639
K2PG	37	-542.8028	1159.6056	0.0081	0.9721
HKYIG	41	-538.8317	1159.6634	0.0079	0.9800
F81I	39	-541.2284	1160.4568	0.0053	0.9853
F81G	39	-541.4186	1160.8372	0.0044	0.9897
K2PIG	38	-542.8024	1161.6048	0.0030	0.9927
HKY	39	-542.1955	1162.3910	0.0020	0.9947
F81IG	40	-541.4752	1162.9503	0.0015	0.9962
JC69I	36	-545.6414	1163.2828	0.0013	0.9975
JC69G	36	-545.8519	1163.7039	0.0010	0.9986
K2P	36	-546.3061	1164.6121	0.0007	0.9992
JC69IG	37	-545.9072	1165.8144	0.0004	0.9996
F81	38	-545.0812	1166.1624	0.0003	0.9999
JC69	35	-549.3415	1168.6830	0.0001	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-542.5724	1282.8112	0.2631	0.2631
K2PG	37	-542.8028	1283.2720	0.2089	0.4720
JC69I	36	-545.6414	1283.6069	0.1767	0.6487
JC69G	36	-545.8519	1284.0279	0.1432	0.7919
K2P	36	-546.3061	1284.9361	0.0909	0.8828
JC69	35	-549.3415	1285.6647	0.0632	0.9460
K2PIG	38	-542.8024	1288.6135	0.0145	0.9605
JC69IG	37	-545.9072	1289.4807	0.0094	0.9698
F81I	39	-541.2284	1290.8078	0.0048	0.9747
HKYI	40	-538.6152	1290.9238	0.0046	0.9792
F81G	39	-541.4186	1291.1882	0.0040	0.9832
HKYG	40	-538.8321	1291.3576	0.0037	0.9869
SYMI	41	-536.2380	1291.5117	0.0034	0.9903
SYM	40	-539.1089	1291.9113	0.0028	0.9930
SYMG	41	-536.4408	1291.9174	0.0028	0.9958
HKY	39	-542.1955	1292.7421	0.0018	0.9976
F81	38	-545.0812	1293.1711	0.0015	0.9991
F81IG	40	-541.4752	1296.6437	0.0003	0.9994
HKYIG	41	-538.8317	1296.6991	0.0003	0.9996
SYMIG	42	-536.4590	1297.2961	0.0002	0.9998
GTRI	44	-532.2342	1299.5312	0.0001	0.9999
GTRG	44	-532.4007	1299.8641	0.0001	0.9999
GTR	43	-535.1052	1299.9308	0.0001	1.0000
GTRIG	45	-532.4171	1305.2393	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_1565.phylip = 1 - 209;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_1565.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 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) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_1565.phylip = 1 - 209;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_1565.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Fixed(Equal) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_1565.phylip = 1 - 209;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr8_1565.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

