
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:56 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/chr3_299.phylip" (19 taxa, 476 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	-1071.0425	2232.0206	0.3630	0.3630
HKYI	40	-1072.4037	2232.3477	0.3082	0.6712
HKYG	40	-1072.5280	2232.5963	0.2722	0.9434
GTRI	44	-1070.0977	2237.3834	0.0249	0.9682
GTRG	44	-1070.4195	2238.0269	0.0180	0.9863
GTRIG	45	-1069.4699	2238.5676	0.0137	1.0000
HKY	39	-1090.5201	2266.1962	0.0000	1.0000
GTR	43	-1090.0387	2274.8366	0.0000	1.0000
F81IG	40	-1095.2444	2278.0291	0.0000	1.0000
F81G	39	-1096.7136	2278.5832	0.0000	1.0000
F81I	39	-1096.7779	2278.7119	0.0000	1.0000
K2PIG	38	-1111.4587	2305.6999	0.0000	1.0000
K2PG	37	-1113.1347	2306.6895	0.0000	1.0000
K2PI	37	-1113.1641	2306.7484	0.0000	1.0000
F81	38	-1112.6085	2307.9995	0.0000	1.0000
SYMIG	42	-1110.3775	2313.0968	0.0000	1.0000
SYMI	41	-1111.9572	2313.8498	0.0000	1.0000
SYMG	41	-1112.0018	2313.9391	0.0000	1.0000
K2P	36	-1129.3227	2336.7138	0.0000	1.0000
JC69IG	37	-1128.8182	2338.0566	0.0000	1.0000
JC69G	36	-1130.4555	2338.9793	0.0000	1.0000
JC69I	36	-1130.6039	2339.2762	0.0000	1.0000
SYM	40	-1128.5234	2344.5871	0.0000	1.0000
JC69	35	-1145.9981	2367.7235	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1071.0425	2224.0851	0.3815	0.3815
HKYI	40	-1072.4037	2224.8075	0.2658	0.6473
HKYG	40	-1072.5280	2225.0561	0.2348	0.8821
GTRI	44	-1070.0977	2228.1955	0.0489	0.9309
GTRG	44	-1070.4195	2228.8390	0.0354	0.9663
GTRIG	45	-1069.4699	2228.9397	0.0337	1.0000
HKY	39	-1090.5201	2259.0402	0.0000	1.0000
GTR	43	-1090.0387	2266.0773	0.0000	1.0000
F81IG	40	-1095.2444	2270.4889	0.0000	1.0000
F81G	39	-1096.7136	2271.4272	0.0000	1.0000
F81I	39	-1096.7779	2271.5559	0.0000	1.0000
K2PIG	38	-1111.4587	2298.9173	0.0000	1.0000
K2PG	37	-1113.1347	2300.2694	0.0000	1.0000
K2PI	37	-1113.1641	2300.3283	0.0000	1.0000
F81	38	-1112.6085	2301.2169	0.0000	1.0000
SYMIG	42	-1110.3775	2304.7550	0.0000	1.0000
SYMI	41	-1111.9572	2305.9143	0.0000	1.0000
SYMG	41	-1112.0018	2306.0036	0.0000	1.0000
K2P	36	-1129.3227	2330.6454	0.0000	1.0000
JC69IG	37	-1128.8182	2331.6365	0.0000	1.0000
JC69G	36	-1130.4555	2332.9109	0.0000	1.0000
JC69I	36	-1130.6039	2333.2078	0.0000	1.0000
SYM	40	-1128.5234	2337.0469	0.0000	1.0000
JC69	35	-1145.9981	2361.9962	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1072.4037	2391.4242	0.4850	0.4850
HKYG	40	-1072.5280	2391.6728	0.4283	0.9133
HKYIG	41	-1071.0425	2394.8672	0.0867	1.0000
GTRI	44	-1070.0977	2411.4738	0.0000	1.0000
GTRG	44	-1070.4195	2412.1173	0.0000	1.0000
GTRIG	45	-1069.4699	2416.3835	0.0000	1.0000
HKY	39	-1090.5201	2421.4915	0.0000	1.0000
F81G	39	-1096.7136	2433.8785	0.0000	1.0000
F81I	39	-1096.7779	2434.0072	0.0000	1.0000
F81IG	40	-1095.2444	2437.1056	0.0000	1.0000
GTR	43	-1090.0387	2445.1903	0.0000	1.0000
K2PG	37	-1113.1347	2454.3899	0.0000	1.0000
K2PI	37	-1113.1641	2454.4487	0.0000	1.0000
K2PIG	38	-1111.4587	2457.2032	0.0000	1.0000
F81	38	-1112.6085	2459.5028	0.0000	1.0000
SYMI	41	-1111.9572	2476.6965	0.0000	1.0000
SYMG	41	-1112.0018	2476.7857	0.0000	1.0000
SYMIG	42	-1110.3775	2479.7025	0.0000	1.0000
K2P	36	-1129.3227	2480.6005	0.0000	1.0000
JC69G	36	-1130.4555	2482.8660	0.0000	1.0000
JC69I	36	-1130.6039	2483.1629	0.0000	1.0000
JC69IG	37	-1128.8182	2485.7569	0.0000	1.0000
SYM	40	-1128.5234	2503.6636	0.0000	1.0000
JC69	35	-1145.9981	2507.7858	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/chr3_299.phylip = 1 - 476;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_299.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/chr3_299.phylip = 1 - 476;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_299.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/chr3_299.phylip = 1 - 476;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr3_299.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

