
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:56 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/chr7_10832.phylip" (19 taxa, 405 characters)

Minimum AIC  model: GTRI
Minimum AICc model: GTRI
Minimum BIC  model: HKYI


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
GTRI	44	-1103.9989	2306.9979	0.2510	0.2510
GTRG	44	-1104.0071	2307.0142	0.2490	0.5000
HKYI	40	-1109.2669	2307.5447	0.1910	0.6910
HKYG	40	-1109.3266	2307.6641	0.1799	0.8709
GTRIG	45	-1103.8816	2309.2953	0.0796	0.9504
HKYIG	41	-1109.3776	2310.2428	0.0496	1.0000
GTR	43	-1117.9705	2332.4230	0.0000	1.0000
HKY	39	-1123.9490	2334.4460	0.0000	1.0000
F81I	39	-1124.3570	2335.2619	0.0000	1.0000
F81G	39	-1124.4681	2335.4841	0.0000	1.0000
F81IG	40	-1124.4678	2337.9465	0.0000	1.0000
K2PI	37	-1130.0317	2341.7256	0.0000	1.0000
K2PG	37	-1130.2202	2342.1026	0.0000	1.0000
K2PIG	38	-1130.2199	2344.5383	0.0000	1.0000
SYMI	41	-1129.2827	2350.0529	0.0000	1.0000
SYMG	41	-1129.4618	2350.4111	0.0000	1.0000
SYMIG	42	-1129.4614	2352.9007	0.0000	1.0000
F81	38	-1138.7244	2361.5471	0.0000	1.0000
JC69I	36	-1143.6735	2366.5861	0.0000	1.0000
JC69G	36	-1143.7604	2366.7600	0.0000	1.0000
JC69IG	37	-1143.7600	2369.1822	0.0000	1.0000
K2P	36	-1145.9367	2371.1124	0.0000	1.0000
SYM	40	-1144.4954	2378.0017	0.0000	1.0000
JC69	35	-1158.9140	2394.6573	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1103.9989	2295.9979	0.3284	0.3284
GTRG	44	-1104.0071	2296.0142	0.3258	0.6542
GTRIG	45	-1103.8816	2297.7632	0.1359	0.7901
HKYI	40	-1109.2669	2298.5337	0.0924	0.8825
HKYG	40	-1109.3266	2298.6531	0.0871	0.9696
HKYIG	41	-1109.3776	2300.7552	0.0304	1.0000
GTR	43	-1117.9705	2321.9410	0.0000	1.0000
HKY	39	-1123.9490	2325.8981	0.0000	1.0000
F81I	39	-1124.3570	2326.7140	0.0000	1.0000
F81G	39	-1124.4681	2326.9362	0.0000	1.0000
F81IG	40	-1124.4678	2328.9355	0.0000	1.0000
K2PI	37	-1130.0317	2334.0634	0.0000	1.0000
K2PG	37	-1130.2202	2334.4404	0.0000	1.0000
K2PIG	38	-1130.2199	2336.4399	0.0000	1.0000
SYMI	41	-1129.2827	2340.5653	0.0000	1.0000
SYMG	41	-1129.4618	2340.9235	0.0000	1.0000
SYMIG	42	-1129.4614	2342.9228	0.0000	1.0000
F81	38	-1138.7244	2353.4487	0.0000	1.0000
JC69I	36	-1143.6735	2359.3470	0.0000	1.0000
JC69G	36	-1143.7604	2359.5209	0.0000	1.0000
JC69IG	37	-1143.7600	2361.5201	0.0000	1.0000
K2P	36	-1145.9367	2363.8733	0.0000	1.0000
SYM	40	-1144.4954	2368.9907	0.0000	1.0000
JC69	35	-1158.9140	2387.8280	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1109.2669	2458.6892	0.5028	0.5028
HKYG	40	-1109.3266	2458.8086	0.4736	0.9764
HKYIG	41	-1109.3776	2464.9146	0.0224	0.9988
GTRI	44	-1103.9989	2472.1689	0.0006	0.9994
GTRG	44	-1104.0071	2472.1852	0.0006	0.9999
GTRIG	45	-1103.8816	2477.9381	0.0000	1.0000
HKY	39	-1123.9490	2482.0497	0.0000	1.0000
K2PI	37	-1130.0317	2482.2073	0.0000	1.0000
K2PG	37	-1130.2202	2482.5843	0.0000	1.0000
F81I	39	-1124.3570	2482.8656	0.0000	1.0000
F81G	39	-1124.4681	2483.0878	0.0000	1.0000
K2PIG	38	-1130.2199	2488.5876	0.0000	1.0000
F81IG	40	-1124.4678	2489.0910	0.0000	1.0000
GTR	43	-1117.9705	2494.1082	0.0000	1.0000
JC69I	36	-1143.6735	2503.4869	0.0000	1.0000
JC69G	36	-1143.7604	2503.6608	0.0000	1.0000
SYMI	41	-1129.2827	2504.7247	0.0000	1.0000
SYMG	41	-1129.4618	2505.0829	0.0000	1.0000
F81	38	-1138.7244	2505.5964	0.0000	1.0000
K2P	36	-1145.9367	2508.0132	0.0000	1.0000
JC69IG	37	-1143.7600	2509.6639	0.0000	1.0000
SYMIG	42	-1129.4614	2511.0861	0.0000	1.0000
JC69	35	-1158.9140	2527.9640	0.0000	1.0000
SYM	40	-1144.4954	2529.1462	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/chr7_10832.phylip = 1 - 405;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10832.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 (GTRI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10832.phylip = 1 - 405;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10832.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 BIC model (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10832.phylip = 1 - 405;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_10832.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

