
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:14 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/chr13_720.phylip" (19 taxa, 455 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
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
HKYI	40	-1060.2517	2208.4261	0.4091	0.4091
HKYG	40	-1060.2656	2208.4538	0.4035	0.8126
HKYIG	41	-1060.1676	2210.6743	0.1329	0.9455
GTRI	44	-1058.2470	2214.1525	0.0234	0.9689
GTRG	44	-1058.2573	2214.1732	0.0231	0.9920
GTRIG	45	-1058.0834	2216.2890	0.0080	1.0000
HKY	39	-1078.2204	2241.9588	0.0000	1.0000
GTR	43	-1076.2485	2247.7039	0.0000	1.0000
F81I	39	-1089.9740	2265.4660	0.0000	1.0000
F81G	39	-1089.9963	2265.5107	0.0000	1.0000
F81IG	40	-1089.8324	2267.5875	0.0000	1.0000
K2PI	37	-1097.3672	2275.4778	0.0000	1.0000
K2PG	37	-1097.4328	2275.6089	0.0000	1.0000
SYMI	41	-1092.8145	2275.9680	0.0000	1.0000
SYMG	41	-1092.8684	2276.0758	0.0000	1.0000
K2PIG	38	-1097.0012	2277.1273	0.0000	1.0000
SYMIG	42	-1092.3404	2277.4477	0.0000	1.0000
F81	38	-1107.4100	2297.9450	0.0000	1.0000
K2P	36	-1115.4545	2309.2821	0.0000	1.0000
SYM	40	-1111.5987	2311.1201	0.0000	1.0000
JC69I	36	-1122.8537	2324.0806	0.0000	1.0000
JC69G	36	-1122.8870	2324.1472	0.0000	1.0000
JC69IG	37	-1122.5681	2325.8796	0.0000	1.0000
JC69	35	-1140.4160	2356.8463	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1060.2517	2200.5034	0.3682	0.3682
HKYG	40	-1060.2656	2200.5311	0.3631	0.7314
HKYIG	41	-1060.1676	2202.3353	0.1473	0.8787
GTRI	44	-1058.2470	2204.4940	0.0501	0.9288
GTRG	44	-1058.2573	2204.5146	0.0496	0.9783
GTRIG	45	-1058.0834	2206.1667	0.0217	1.0000
HKY	39	-1078.2204	2234.4408	0.0000	1.0000
GTR	43	-1076.2485	2238.4971	0.0000	1.0000
F81I	39	-1089.9740	2257.9480	0.0000	1.0000
F81G	39	-1089.9963	2257.9926	0.0000	1.0000
F81IG	40	-1089.8324	2259.6648	0.0000	1.0000
SYMI	41	-1092.8145	2267.6290	0.0000	1.0000
SYMG	41	-1092.8684	2267.7368	0.0000	1.0000
SYMIG	42	-1092.3404	2268.6807	0.0000	1.0000
K2PI	37	-1097.3672	2268.7344	0.0000	1.0000
K2PG	37	-1097.4328	2268.8655	0.0000	1.0000
K2PIG	38	-1097.0012	2270.0023	0.0000	1.0000
F81	38	-1107.4100	2290.8200	0.0000	1.0000
K2P	36	-1115.4545	2302.9089	0.0000	1.0000
SYM	40	-1111.5987	2303.1974	0.0000	1.0000
JC69I	36	-1122.8537	2317.7074	0.0000	1.0000
JC69G	36	-1122.8870	2317.7740	0.0000	1.0000
JC69IG	37	-1122.5681	2319.1362	0.0000	1.0000
JC69	35	-1140.4160	2350.8320	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1060.2517	2365.3153	0.4908	0.4908
HKYG	40	-1060.2656	2365.3430	0.4841	0.9749
HKYIG	41	-1060.1676	2371.2675	0.0250	1.0000
GTRI	44	-1058.2470	2385.7871	0.0000	1.0000
GTRG	44	-1058.2573	2385.8077	0.0000	1.0000
GTRIG	45	-1058.0834	2391.5801	0.0000	1.0000
HKY	39	-1078.2204	2395.1324	0.0000	1.0000
GTR	43	-1076.2485	2415.6698	0.0000	1.0000
F81I	39	-1089.9740	2418.6396	0.0000	1.0000
F81G	39	-1089.9963	2418.6842	0.0000	1.0000
K2PI	37	-1097.3672	2421.1854	0.0000	1.0000
K2PG	37	-1097.4328	2421.3165	0.0000	1.0000
F81IG	40	-1089.8324	2424.4767	0.0000	1.0000
K2PIG	38	-1097.0012	2426.5736	0.0000	1.0000
SYMI	41	-1092.8145	2436.5612	0.0000	1.0000
SYMG	41	-1092.8684	2436.6690	0.0000	1.0000
SYMIG	42	-1092.3404	2441.7332	0.0000	1.0000
F81	38	-1107.4100	2447.3913	0.0000	1.0000
K2P	36	-1115.4545	2451.2396	0.0000	1.0000
JC69I	36	-1122.8537	2466.0381	0.0000	1.0000
JC69G	36	-1122.8870	2466.1047	0.0000	1.0000
SYM	40	-1111.5987	2468.0093	0.0000	1.0000
JC69IG	37	-1122.5681	2471.5872	0.0000	1.0000
JC69	35	-1140.4160	2495.0424	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_720.phylip = 1 - 455;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_720.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;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_720.phylip = 1 - 455;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_720.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;


[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/chr13_720.phylip = 1 - 455;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr13_720.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

