
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:54 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/chr5_10384.phylip" (19 taxa, 409 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	-1080.3027	2249.5183	0.6042	0.6042
GTRI	44	-1076.7679	2252.4149	0.1420	0.7462
HKYIG	41	-1080.6496	2252.6834	0.1241	0.8703
HKYG	40	-1082.4396	2253.7923	0.0713	0.9416
GTRG	44	-1078.2479	2255.3750	0.0323	0.9739
GTRIG	45	-1077.1994	2255.8037	0.0261	1.0000
HKY	39	-1092.6256	2271.7066	0.0000	1.0000
GTR	43	-1088.1215	2272.6101	0.0000	1.0000
F81I	39	-1098.4964	2283.4480	0.0000	1.0000
F81IG	40	-1098.7816	2286.4763	0.0000	1.0000
F81G	39	-1100.4225	2287.3003	0.0000	1.0000
K2PIG	38	-1102.0723	2288.1555	0.0000	1.0000
K2PI	37	-1103.6208	2288.8211	0.0000	1.0000
K2PG	37	-1103.9066	2289.3927	0.0000	1.0000
SYMI	41	-1099.8695	2291.1233	0.0000	1.0000
SYMG	41	-1101.4077	2294.1995	0.0000	1.0000
SYMIG	42	-1100.2344	2294.3377	0.0000	1.0000
F81	38	-1110.6398	2305.2905	0.0000	1.0000
K2P	36	-1114.8760	2308.9133	0.0000	1.0000
SYM	40	-1112.2032	2313.3195	0.0000	1.0000
JC69I	36	-1117.7235	2314.6083	0.0000	1.0000
JC69IG	37	-1117.9643	2317.5081	0.0000	1.0000
JC69G	36	-1119.6268	2318.4148	0.0000	1.0000
JC69	35	-1130.3316	2337.4193	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-1080.3027	2240.6053	0.4350	0.4350
GTRI	44	-1076.7679	2241.5357	0.2732	0.7081
HKYIG	41	-1080.6496	2243.2992	0.1131	0.8212
GTRIG	45	-1077.1994	2244.3987	0.0653	0.8865
GTRG	44	-1078.2479	2244.4959	0.0622	0.9487
HKYG	40	-1082.4396	2244.8793	0.0513	1.0000
GTR	43	-1088.1215	2262.2430	0.0000	1.0000
HKY	39	-1092.6256	2263.2513	0.0000	1.0000
F81I	39	-1098.4964	2274.9927	0.0000	1.0000
F81IG	40	-1098.7816	2277.5632	0.0000	1.0000
F81G	39	-1100.4225	2278.8451	0.0000	1.0000
K2PIG	38	-1102.0723	2280.1447	0.0000	1.0000
K2PI	37	-1103.6208	2281.2416	0.0000	1.0000
SYMI	41	-1099.8695	2281.7391	0.0000	1.0000
K2PG	37	-1103.9066	2281.8131	0.0000	1.0000
SYMIG	42	-1100.2344	2284.4688	0.0000	1.0000
SYMG	41	-1101.4077	2284.8153	0.0000	1.0000
F81	38	-1110.6398	2297.2796	0.0000	1.0000
K2P	36	-1114.8760	2301.7520	0.0000	1.0000
SYM	40	-1112.2032	2304.4065	0.0000	1.0000
JC69I	36	-1117.7235	2307.4470	0.0000	1.0000
JC69IG	37	-1117.9643	2309.9285	0.0000	1.0000
JC69G	36	-1119.6268	2311.2535	0.0000	1.0000
JC69	35	-1130.3316	2330.6632	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1080.3027	2401.1539	0.8671	0.8671
HKYG	40	-1082.4396	2405.4279	0.1023	0.9694
HKYIG	41	-1080.6496	2407.8616	0.0303	0.9997
GTRI	44	-1076.7679	2418.1392	0.0002	0.9999
HKY	39	-1092.6256	2419.7862	0.0001	1.0000
GTRG	44	-1078.2479	2421.0994	0.0000	1.0000
GTRIG	45	-1077.1994	2425.0159	0.0000	1.0000
K2PI	37	-1103.6208	2429.7490	0.0000	1.0000
K2PG	37	-1103.9066	2430.3206	0.0000	1.0000
F81I	39	-1098.4964	2431.5276	0.0000	1.0000
K2PIG	38	-1102.0723	2432.6659	0.0000	1.0000
GTR	43	-1088.1215	2434.8328	0.0000	1.0000
F81G	39	-1100.4225	2435.3800	0.0000	1.0000
F81IG	40	-1098.7816	2438.1118	0.0000	1.0000
K2P	36	-1114.8760	2446.2457	0.0000	1.0000
SYMI	41	-1099.8695	2446.3014	0.0000	1.0000
SYMG	41	-1101.4077	2449.3776	0.0000	1.0000
F81	38	-1110.6398	2449.8008	0.0000	1.0000
JC69I	36	-1117.7235	2451.9407	0.0000	1.0000
SYMIG	42	-1100.2344	2453.0449	0.0000	1.0000
JC69G	36	-1119.6268	2455.7473	0.0000	1.0000
JC69IG	37	-1117.9643	2458.4360	0.0000	1.0000
SYM	40	-1112.2032	2464.9551	0.0000	1.0000
JC69	35	-1130.3316	2471.1433	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/chr5_10384.phylip = 1 - 409;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10384.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/chr5_10384.phylip = 1 - 409;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10384.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/chr5_10384.phylip = 1 - 409;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr5_10384.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

