
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:38 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/chr1_2557.phylip" (19 taxa, 359 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	-1212.9833	2526.5781	0.6580	0.6580
HKYI	40	-1219.9717	2530.2578	0.1045	0.7625
HKYG	40	-1219.9942	2530.3028	0.1022	0.8647
GTRG	44	-1215.0417	2530.6949	0.0840	0.9487
HKYIG	41	-1219.9938	2532.8519	0.0286	0.9773
GTRIG	45	-1215.0420	2533.3109	0.0227	1.0000
K2PI	37	-1239.2923	2561.3447	0.0000	1.0000
SYMI	41	-1234.3565	2561.5774	0.0000	1.0000
K2PG	37	-1239.6124	2561.9849	0.0000	1.0000
SYMG	41	-1235.2169	2563.2982	0.0000	1.0000
F81I	39	-1238.0145	2563.8096	0.0000	1.0000
K2PIG	38	-1239.6122	2564.4869	0.0000	1.0000
F81G	39	-1238.6883	2565.1572	0.0000	1.0000
SYMIG	42	-1235.2169	2565.8642	0.0000	1.0000
F81IG	40	-1238.9095	2568.1335	0.0000	1.0000
JC69I	36	-1255.4796	2591.2325	0.0000	1.0000
JC69G	36	-1255.9118	2592.0969	0.0000	1.0000
JC69IG	37	-1255.4307	2593.6215	0.0000	1.0000
HKY	39	-1255.8892	2599.5589	0.0000	1.0000
GTR	43	-1251.4022	2600.8171	0.0000	1.0000
K2P	36	-1272.3487	2624.9707	0.0000	1.0000
F81	38	-1270.1392	2625.5409	0.0000	1.0000
SYM	40	-1267.9937	2626.3019	0.0000	1.0000
JC69	35	-1285.8644	2649.5306	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1212.9833	2513.9667	0.7738	0.7738
GTRG	44	-1215.0417	2518.0834	0.0988	0.8726
HKYI	40	-1219.9717	2519.9434	0.0390	0.9115
HKYG	40	-1219.9942	2519.9883	0.0381	0.9496
GTRIG	45	-1215.0420	2520.0840	0.0363	0.9860
HKYIG	41	-1219.9938	2521.9876	0.0140	1.0000
SYMI	41	-1234.3565	2550.7131	0.0000	1.0000
SYMG	41	-1235.2169	2552.4339	0.0000	1.0000
K2PI	37	-1239.2923	2552.5846	0.0000	1.0000
K2PG	37	-1239.6124	2553.2248	0.0000	1.0000
F81I	39	-1238.0145	2554.0290	0.0000	1.0000
SYMIG	42	-1235.2169	2554.4338	0.0000	1.0000
K2PIG	38	-1239.6122	2555.2244	0.0000	1.0000
F81G	39	-1238.6883	2555.3767	0.0000	1.0000
F81IG	40	-1238.9095	2557.8191	0.0000	1.0000
JC69I	36	-1255.4796	2582.9592	0.0000	1.0000
JC69G	36	-1255.9118	2583.8236	0.0000	1.0000
JC69IG	37	-1255.4307	2584.8613	0.0000	1.0000
GTR	43	-1251.4022	2588.8044	0.0000	1.0000
HKY	39	-1255.8892	2589.7784	0.0000	1.0000
SYM	40	-1267.9937	2615.9874	0.0000	1.0000
F81	38	-1270.1392	2616.2784	0.0000	1.0000
K2P	36	-1272.3487	2616.6974	0.0000	1.0000
JC69	35	-1285.8644	2641.7287	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1219.9717	2675.2763	0.4904	0.4904
HKYG	40	-1219.9942	2675.3212	0.4795	0.9700
HKYIG	41	-1219.9938	2681.2038	0.0253	0.9953
GTRI	44	-1212.9833	2684.8329	0.0041	0.9994
GTRG	44	-1215.0417	2688.9496	0.0005	0.9999
GTRIG	45	-1215.0420	2694.8335	0.0000	1.0000
K2PI	37	-1239.2923	2696.2675	0.0000	1.0000
K2PG	37	-1239.6124	2696.9077	0.0000	1.0000
K2PIG	38	-1239.6122	2702.7906	0.0000	1.0000
F81I	39	-1238.0145	2705.4786	0.0000	1.0000
F81G	39	-1238.6883	2706.8263	0.0000	1.0000
SYMI	41	-1234.3565	2709.9293	0.0000	1.0000
SYMG	41	-1235.2169	2711.6501	0.0000	1.0000
F81IG	40	-1238.9095	2713.1520	0.0000	1.0000
SYMIG	42	-1235.2169	2717.5334	0.0000	1.0000
JC69I	36	-1255.4796	2722.7588	0.0000	1.0000
JC69G	36	-1255.9118	2723.6232	0.0000	1.0000
JC69IG	37	-1255.4307	2728.5443	0.0000	1.0000
HKY	39	-1255.8892	2741.2279	0.0000	1.0000
GTR	43	-1251.4022	2755.7873	0.0000	1.0000
K2P	36	-1272.3487	2756.4970	0.0000	1.0000
F81	38	-1270.1392	2763.8446	0.0000	1.0000
SYM	40	-1267.9937	2771.3203	0.0000	1.0000
JC69	35	-1285.8644	2777.6450	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/chr1_2557.phylip = 1 - 359;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_2557.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/chr1_2557.phylip = 1 - 359;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_2557.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/chr1_2557.phylip = 1 - 359;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_2557.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;


-------------------------------------------------------------
End of Output

