
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:07 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/chr10_5708.phylip" (19 taxa, 413 characters)

Minimum AIC  model: GTRI
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	-1160.5180	2409.8532	0.2284	0.2284
GTRI	44	-1155.5950	2409.9508	0.2176	0.4460
HKYG	40	-1160.5685	2409.9541	0.2172	0.6632
GTRG	44	-1155.8308	2410.4224	0.1719	0.8351
HKYIG	41	-1160.1473	2411.5777	0.0965	0.9315
GTRIG	45	-1155.4912	2412.2630	0.0685	1.0000
K2PI	37	-1175.5008	2432.5002	0.0000	1.0000
K2PG	37	-1176.2769	2434.0524	0.0000	1.0000
K2PIG	38	-1175.8774	2435.6799	0.0000	1.0000
SYMI	41	-1172.9231	2437.1292	0.0000	1.0000
SYMG	41	-1173.6819	2438.6468	0.0000	1.0000
SYMIG	42	-1173.7719	2441.3060	0.0000	1.0000
GTR	43	-1175.2875	2446.8298	0.0000	1.0000
HKY	39	-1181.1406	2448.6457	0.0000	1.0000
F81I	39	-1185.7203	2457.8051	0.0000	1.0000
F81G	39	-1186.2873	2458.9392	0.0000	1.0000
F81IG	40	-1186.3241	2461.4654	0.0000	1.0000
K2P	36	-1195.7504	2470.5859	0.0000	1.0000
SYM	40	-1192.5130	2473.8432	0.0000	1.0000
JC69I	36	-1198.9625	2477.0102	0.0000	1.0000
JC69G	36	-1199.5130	2478.1110	0.0000	1.0000
JC69IG	37	-1199.5128	2480.5242	0.0000	1.0000
F81	38	-1205.6749	2495.2749	0.0000	1.0000
JC69	35	-1218.6834	2514.0511	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRI	44	-1155.5950	2399.1899	0.3140	0.3140
GTRG	44	-1155.8308	2399.6616	0.2480	0.5620
GTRIG	45	-1155.4912	2400.9823	0.1281	0.6902
HKYI	40	-1160.5180	2401.0360	0.1248	0.8149
HKYG	40	-1160.5685	2401.1369	0.1186	0.9335
HKYIG	41	-1160.1473	2402.2947	0.0665	1.0000
K2PI	37	-1175.5008	2425.0016	0.0000	1.0000
K2PG	37	-1176.2769	2426.5537	0.0000	1.0000
K2PIG	38	-1175.8774	2427.7548	0.0000	1.0000
SYMI	41	-1172.9231	2427.8461	0.0000	1.0000
SYMG	41	-1173.6819	2429.3637	0.0000	1.0000
SYMIG	42	-1173.7719	2431.5438	0.0000	1.0000
GTR	43	-1175.2875	2436.5751	0.0000	1.0000
HKY	39	-1181.1406	2440.2811	0.0000	1.0000
F81I	39	-1185.7203	2449.4405	0.0000	1.0000
F81G	39	-1186.2873	2450.5746	0.0000	1.0000
F81IG	40	-1186.3241	2452.6482	0.0000	1.0000
K2P	36	-1195.7504	2463.5008	0.0000	1.0000
SYM	40	-1192.5130	2465.0260	0.0000	1.0000
JC69I	36	-1198.9625	2469.9251	0.0000	1.0000
JC69G	36	-1199.5130	2471.0259	0.0000	1.0000
JC69IG	37	-1199.5128	2473.0256	0.0000	1.0000
F81	38	-1205.6749	2487.3497	0.0000	1.0000
JC69	35	-1218.6834	2507.3668	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-1160.5180	2561.9739	0.4932	0.4932
HKYG	40	-1160.5685	2562.0748	0.4689	0.9622
HKYIG	41	-1160.1473	2567.2561	0.0352	0.9973
K2PI	37	-1175.5008	2573.8691	0.0013	0.9986
K2PG	37	-1176.2769	2575.4213	0.0006	0.9992
GTRI	44	-1155.5950	2576.2216	0.0004	0.9996
GTRG	44	-1155.8308	2576.6933	0.0003	0.9999
K2PIG	38	-1175.8774	2580.6458	0.0000	1.0000
GTRIG	45	-1155.4912	2582.0374	0.0000	1.0000
SYMI	41	-1172.9231	2592.8075	0.0000	1.0000
SYMG	41	-1173.6819	2594.3251	0.0000	1.0000
HKY	39	-1181.1406	2597.1956	0.0000	1.0000
SYMIG	42	-1173.7719	2600.5286	0.0000	1.0000
F81I	39	-1185.7203	2606.3550	0.0000	1.0000
F81G	39	-1186.2873	2607.4891	0.0000	1.0000
K2P	36	-1195.7504	2608.3449	0.0000	1.0000
GTR	43	-1175.2875	2609.5833	0.0000	1.0000
F81IG	40	-1186.3241	2613.5861	0.0000	1.0000
JC69I	36	-1198.9625	2614.7692	0.0000	1.0000
JC69G	36	-1199.5130	2615.8701	0.0000	1.0000
JC69IG	37	-1199.5128	2621.8931	0.0000	1.0000
SYM	40	-1192.5130	2625.9639	0.0000	1.0000
F81	38	-1205.6749	2640.2407	0.0000	1.0000
JC69	35	-1218.6834	2648.1874	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/chr10_5708.phylip = 1 - 413;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_5708.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 (HKYI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_5708.phylip = 1 - 413;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_5708.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/chr10_5708.phylip = 1 - 413;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr10_5708.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

