
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:04 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_32215.phylip" (19 taxa, 491 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	-1175.8356	2441.3415	0.4490	0.4490
HKYI	40	-1177.5910	2442.4708	0.2553	0.7042
HKYG	40	-1177.6611	2442.6112	0.2380	0.9422
GTRIG	45	-1173.7045	2446.7124	0.0306	0.9728
GTRG	44	-1175.6487	2448.1764	0.0147	0.9876
GTRI	44	-1175.8171	2448.5131	0.0124	1.0000
K2PIG	38	-1193.4286	2469.4147	0.0000	1.0000
F81IG	40	-1191.1377	2469.5644	0.0000	1.0000
K2PI	37	-1195.0940	2470.3955	0.0000	1.0000
K2PG	37	-1195.3239	2470.8553	0.0000	1.0000
F81G	39	-1192.9911	2470.9001	0.0000	1.0000
F81I	39	-1193.1174	2471.1528	0.0000	1.0000
SYMIG	42	-1192.1517	2476.3659	0.0000	1.0000
SYMI	41	-1194.3557	2478.3818	0.0000	1.0000
SYMG	41	-1194.3677	2478.4059	0.0000	1.0000
HKY	39	-1199.7416	2484.4012	0.0000	1.0000
GTR	43	-1196.6446	2487.7546	0.0000	1.0000
JC69IG	37	-1207.4974	2495.2023	0.0000	1.0000
JC69G	36	-1209.4417	2496.7512	0.0000	1.0000
JC69I	36	-1209.4808	2496.8295	0.0000	1.0000
F81	38	-1213.5706	2509.6988	0.0000	1.0000
K2P	36	-1218.0179	2513.9037	0.0000	1.0000
SYM	40	-1215.6761	2518.6411	0.0000	1.0000
JC69	35	-1230.2961	2536.1306	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYIG	41	-1175.8356	2433.6711	0.4602	0.4602
HKYI	40	-1177.5910	2435.1820	0.2162	0.6765
HKYG	40	-1177.6611	2435.3223	0.2016	0.8780
GTRIG	45	-1173.7045	2437.4091	0.0710	0.9490
GTRG	44	-1175.6487	2439.2974	0.0276	0.9767
GTRI	44	-1175.8171	2439.6342	0.0233	1.0000
F81IG	40	-1191.1377	2462.2755	0.0000	1.0000
K2PIG	38	-1193.4286	2462.8572	0.0000	1.0000
F81G	39	-1192.9911	2463.9821	0.0000	1.0000
K2PI	37	-1195.0940	2464.1880	0.0000	1.0000
F81I	39	-1193.1174	2464.2348	0.0000	1.0000
K2PG	37	-1195.3239	2464.6478	0.0000	1.0000
SYMIG	42	-1192.1517	2468.3034	0.0000	1.0000
SYMI	41	-1194.3557	2470.7114	0.0000	1.0000
SYMG	41	-1194.3677	2470.7355	0.0000	1.0000
HKY	39	-1199.7416	2477.4832	0.0000	1.0000
GTR	43	-1196.6446	2479.2893	0.0000	1.0000
JC69IG	37	-1207.4974	2488.9948	0.0000	1.0000
JC69G	36	-1209.4417	2490.8834	0.0000	1.0000
JC69I	36	-1209.4808	2490.9617	0.0000	1.0000
F81	38	-1213.5706	2503.1413	0.0000	1.0000
K2P	36	-1218.0179	2508.0359	0.0000	1.0000
SYM	40	-1215.6761	2511.3522	0.0000	1.0000
JC69	35	-1230.2961	2530.5921	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1177.5910	2603.0397	0.4558	0.4558
HKYG	40	-1177.6611	2603.1801	0.4249	0.8807
HKYIG	41	-1175.8356	2605.7253	0.1190	0.9997
K2PI	37	-1195.0940	2619.4564	0.0001	0.9998
K2PG	37	-1195.3239	2619.9162	0.0001	0.9999
K2PIG	38	-1193.4286	2622.3221	0.0000	1.0000
GTRG	44	-1175.6487	2623.9410	0.0000	1.0000
GTRI	44	-1175.8171	2624.2777	0.0000	1.0000
GTRIG	45	-1173.7045	2626.2490	0.0000	1.0000
F81G	39	-1192.9911	2627.6434	0.0000	1.0000
F81I	39	-1193.1174	2627.8962	0.0000	1.0000
F81IG	40	-1191.1377	2630.1332	0.0000	1.0000
HKY	39	-1199.7416	2641.1445	0.0000	1.0000
JC69G	36	-1209.4417	2641.9554	0.0000	1.0000
JC69I	36	-1209.4808	2642.0337	0.0000	1.0000
SYMI	41	-1194.3557	2642.7656	0.0000	1.0000
SYMG	41	-1194.3677	2642.7897	0.0000	1.0000
JC69IG	37	-1207.4974	2644.2633	0.0000	1.0000
SYMIG	42	-1192.1517	2644.5541	0.0000	1.0000
K2P	36	-1218.0179	2659.1079	0.0000	1.0000
GTR	43	-1196.6446	2659.7364	0.0000	1.0000
F81	38	-1213.5706	2662.6061	0.0000	1.0000
JC69	35	-1230.2961	2677.4677	0.0000	1.0000
SYM	40	-1215.6761	2679.2100	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/chr1_32215.phylip = 1 - 491;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32215.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/chr1_32215.phylip = 1 - 491;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32215.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/chr1_32215.phylip = 1 - 491;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr1_32215.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

