
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:00 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_23670.phylip" (19 taxa, 458 characters)

Minimum AIC  model: HKYIG
Minimum AICc model: HKYIG
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
HKYIG	41	-1112.9283	2316.1355	0.3647	0.3647
HKYI	40	-1114.7687	2317.4030	0.1935	0.5581
HKYG	40	-1114.8822	2317.6302	0.1727	0.7309
GTRIG	45	-1108.9984	2318.0453	0.1403	0.8712
GTRI	44	-1110.9464	2319.4812	0.0685	0.9397
GTRG	44	-1111.0802	2319.7487	0.0599	0.9995
F81IG	40	-1121.7166	2331.2989	0.0002	0.9997
F81I	39	-1123.4338	2332.3317	0.0001	0.9998
F81G	39	-1123.5674	2332.5989	0.0001	0.9999
K2PIG	38	-1126.3304	2335.7347	0.0000	0.9999
SYMIG	42	-1121.9126	2336.5289	0.0000	1.0000
K2PI	37	-1127.9708	2336.6369	0.0000	1.0000
K2PG	37	-1128.1381	2336.9714	0.0000	1.0000
SYMI	41	-1123.6247	2337.5283	0.0000	1.0000
SYMG	41	-1123.8649	2338.0087	0.0000	1.0000
JC69IG	37	-1134.4536	2349.6025	0.0000	1.0000
JC69I	36	-1136.0397	2350.4072	0.0000	1.0000
JC69G	36	-1136.2220	2350.7719	0.0000	1.0000
HKY	39	-1136.2335	2357.9310	0.0000	1.0000
GTR	43	-1132.9206	2360.9812	0.0000	1.0000
F81	38	-1144.9382	2372.9505	0.0000	1.0000
K2P	36	-1149.6880	2377.7038	0.0000	1.0000
SYM	40	-1146.0840	2380.0336	0.0000	1.0000
JC69	35	-1157.8819	2391.7353	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1112.9283	2307.8566	0.2918	0.2918
GTRIG	45	-1108.9984	2307.9968	0.2720	0.5638
HKYI	40	-1114.7687	2309.5373	0.1259	0.6897
HKYG	40	-1114.8822	2309.7645	0.1124	0.8021
GTRI	44	-1110.9464	2309.8928	0.1054	0.9075
GTRG	44	-1111.0802	2310.1603	0.0922	0.9997
F81IG	40	-1121.7166	2323.4332	0.0001	0.9998
F81I	39	-1123.4338	2324.8676	0.0001	0.9999
F81G	39	-1123.5674	2325.1348	0.0001	1.0000
SYMIG	42	-1121.9126	2327.8253	0.0000	1.0000
K2PIG	38	-1126.3304	2328.6607	0.0000	1.0000
SYMI	41	-1123.6247	2329.2495	0.0000	1.0000
SYMG	41	-1123.8649	2329.7299	0.0000	1.0000
K2PI	37	-1127.9708	2329.9417	0.0000	1.0000
K2PG	37	-1128.1381	2330.2761	0.0000	1.0000
JC69IG	37	-1134.4536	2342.9072	0.0000	1.0000
JC69I	36	-1136.0397	2344.0794	0.0000	1.0000
JC69G	36	-1136.2220	2344.4441	0.0000	1.0000
HKY	39	-1136.2335	2350.4669	0.0000	1.0000
GTR	43	-1132.9206	2351.8411	0.0000	1.0000
F81	38	-1144.9382	2365.8765	0.0000	1.0000
K2P	36	-1149.6880	2371.3760	0.0000	1.0000
SYM	40	-1146.0840	2372.1679	0.0000	1.0000
JC69	35	-1157.8819	2385.7637	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1114.7687	2474.6121	0.4478	0.4478
HKYG	40	-1114.8822	2474.8392	0.3997	0.8474
HKYIG	41	-1112.9283	2477.0583	0.1318	0.9792
K2PI	37	-1127.9708	2482.6358	0.0081	0.9873
K2PG	37	-1128.1381	2482.9703	0.0069	0.9942
K2PIG	38	-1126.3304	2485.4817	0.0020	0.9961
F81I	39	-1123.4338	2485.8155	0.0017	0.9978
F81G	39	-1123.5674	2486.0827	0.0014	0.9992
F81IG	40	-1121.7166	2488.5080	0.0004	0.9997
GTRI	44	-1110.9464	2491.4751	0.0001	0.9998
GTRG	44	-1111.0802	2491.7426	0.0001	0.9998
JC69I	36	-1136.0397	2492.6467	0.0001	0.9999
JC69G	36	-1136.2220	2493.0114	0.0000	0.9999
GTRIG	45	-1108.9984	2493.7059	0.0000	1.0000
JC69IG	37	-1134.4536	2495.6014	0.0000	1.0000
SYMI	41	-1123.6247	2498.4511	0.0000	1.0000
SYMG	41	-1123.8649	2498.9315	0.0000	1.0000
SYMIG	42	-1121.9126	2501.1538	0.0000	1.0000
HKY	39	-1136.2335	2511.4148	0.0000	1.0000
K2P	36	-1149.6880	2519.9433	0.0000	1.0000
F81	38	-1144.9382	2522.6975	0.0000	1.0000
GTR	43	-1132.9206	2529.2965	0.0000	1.0000
JC69	35	-1157.8819	2530.2042	0.0000	1.0000
SYM	40	-1146.0840	2537.2427	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23670.phylip = 1 - 458;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23670.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23670.phylip = 1 - 458;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23670.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=invgamma;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0) 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/chr2_23670.phylip = 1 - 458;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_23670.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

