
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:28 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/chr1_5277.phylip" (19 taxa, 253 characters)

Minimum AIC  model: GTR
Minimum AICc model: GTR
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
GTR	43	-586.7390	1277.5833	0.2415	0.2415
GTRG	44	-586.0938	1279.2261	0.1062	0.3478
GTRI	44	-586.1342	1279.3069	0.1020	0.4498
SYM	40	-592.0175	1279.5067	0.0923	0.5421
K2P	36	-597.7097	1279.7528	0.0816	0.6238
K2PG	37	-596.7171	1280.5132	0.0558	0.6796
HKY	39	-593.9888	1280.6256	0.0528	0.7324
SYMG	41	-591.2438	1280.8098	0.0481	0.7805
K2PI	37	-596.9188	1280.9167	0.0456	0.8261
SYMI	41	-591.3117	1280.9457	0.0450	0.8711
HKYG	40	-593.1409	1281.7534	0.0300	0.9011
HKYI	40	-593.2767	1282.0251	0.0262	0.9273
GTRIG	45	-586.0971	1282.1941	0.0241	0.9514
K2PIG	38	-596.7125	1283.2754	0.0140	0.9654
SYMIG	42	-591.2467	1283.6934	0.0114	0.9768
HKYIG	41	-593.1388	1284.5999	0.0072	0.9841
JC69	35	-601.9690	1285.5509	0.0045	0.9885
F81	38	-598.1438	1286.1380	0.0034	0.9919
JC69G	36	-601.2986	1286.9306	0.0023	0.9942
JC69I	36	-601.3549	1287.0432	0.0021	0.9963
F81G	39	-597.6044	1287.8567	0.0014	0.9977
F81I	39	-597.6329	1287.9136	0.0014	0.9991
JC69IG	37	-601.3028	1289.6847	0.0006	0.9997
F81IG	40	-597.6078	1290.6874	0.0003	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTR	43	-586.7390	1259.4780	0.3224	0.3224
GTRG	44	-586.0938	1260.1876	0.2261	0.5485
GTRI	44	-586.1342	1260.2684	0.2172	0.7657
GTRIG	45	-586.0971	1262.1941	0.0829	0.8486
SYM	40	-592.0175	1264.0350	0.0330	0.8816
SYMG	41	-591.2438	1264.4875	0.0263	0.9079
SYMI	41	-591.3117	1264.6234	0.0246	0.9325
HKY	39	-593.9888	1265.9777	0.0125	0.9450
HKYG	40	-593.1409	1266.2817	0.0107	0.9558
SYMIG	42	-591.2467	1266.4934	0.0097	0.9654
HKYI	40	-593.2767	1266.5534	0.0094	0.9748
K2P	36	-597.7097	1267.4195	0.0061	0.9809
K2PG	37	-596.7171	1267.4341	0.0060	0.9869
K2PI	37	-596.9188	1267.8376	0.0049	0.9919
HKYIG	41	-593.1388	1268.2776	0.0040	0.9958
K2PIG	38	-596.7125	1269.4249	0.0022	0.9981
F81	38	-598.1438	1272.2875	0.0005	0.9986
F81G	39	-597.6044	1273.2088	0.0003	0.9989
F81I	39	-597.6329	1273.2658	0.0003	0.9993
JC69	35	-601.9690	1273.9380	0.0002	0.9995
JC69G	36	-601.2986	1274.5973	0.0002	0.9997
JC69I	36	-601.3549	1274.7098	0.0002	0.9998
F81IG	40	-597.6078	1275.2157	0.0001	0.9999
JC69IG	37	-601.3028	1276.6057	0.0001	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-597.7097	1394.6215	0.6166	0.6166
JC69	35	-601.9690	1397.6067	0.1386	0.7552
K2PG	37	-596.7171	1398.1696	0.1046	0.8598
K2PI	37	-596.9188	1398.5730	0.0855	0.9453
JC69G	36	-601.2986	1401.7993	0.0170	0.9624
JC69I	36	-601.3549	1401.9118	0.0161	0.9785
K2PIG	38	-596.7125	1403.6937	0.0066	0.9851
HKY	39	-593.9888	1403.7799	0.0063	0.9914
SYM	40	-592.0175	1405.3706	0.0029	0.9943
F81	38	-598.1438	1406.5563	0.0016	0.9958
JC69IG	37	-601.3028	1407.3411	0.0011	0.9969
HKYG	40	-593.1409	1407.6173	0.0009	0.9978
HKYI	40	-593.2767	1407.8889	0.0008	0.9986
SYMG	41	-591.2438	1409.3565	0.0004	0.9990
SYMI	41	-591.3117	1409.4923	0.0004	0.9994
F81G	39	-597.6044	1411.0110	0.0002	0.9996
F81I	39	-597.6329	1411.0680	0.0002	0.9997
GTR	43	-586.7390	1411.4138	0.0001	0.9999
HKYIG	41	-593.1388	1413.1465	0.0001	0.9999
SYMIG	42	-591.2467	1414.8958	0.0000	1.0000
GTRG	44	-586.0938	1415.6568	0.0000	1.0000
GTRI	44	-586.1342	1415.7376	0.0000	1.0000
F81IG	40	-597.6078	1416.5513	0.0000	1.0000
GTRIG	45	-586.0971	1421.1967	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5277.phylip = 1 - 253;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5277.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=Dirichlet(1.0,1.0,1.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5277.phylip = 1 - 253;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5277.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=Dirichlet(1.0,1.0,1.0,1.0);
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/chr1_5277.phylip = 1 - 253;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_5277.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

