
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:25 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/chr4_9731.phylip" (19 taxa, 364 characters)

Minimum AIC  model: HKYG
Minimum AICc model: HKYG
Minimum BIC  model: HKYG


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
HKYG	40	-1202.5009	2495.1565	0.5355	0.5355
HKYI	40	-1203.1001	2496.3551	0.2941	0.8297
HKYIG	41	-1202.4915	2497.6787	0.1517	0.9814
GTRG	44	-1201.3343	2503.0825	0.0102	0.9916
GTRI	44	-1201.9327	2504.2791	0.0056	0.9972
GTRIG	45	-1201.3184	2505.6557	0.0028	1.0000
K2PG	37	-1219.8705	2522.3667	0.0000	1.0000
K2PI	37	-1220.5408	2523.7074	0.0000	1.0000
HKY	39	-1218.5382	2524.7060	0.0000	1.0000
K2PIG	38	-1219.8596	2524.8392	0.0000	1.0000
SYMG	41	-1219.4257	2531.5470	0.0000	1.0000
GTR	43	-1217.4507	2532.7265	0.0000	1.0000
SYMI	41	-1220.1296	2532.9548	0.0000	1.0000
SYMIG	42	-1219.4123	2534.0769	0.0000	1.0000
K2P	36	-1236.1478	2552.4425	0.0000	1.0000
SYM	40	-1235.7947	2561.7442	0.0000	1.0000
F81G	39	-1238.0133	2563.6563	0.0000	1.0000
F81I	39	-1238.5554	2564.7403	0.0000	1.0000
F81IG	40	-1238.0104	2566.1757	0.0000	1.0000
JC69G	36	-1251.9287	2584.0041	0.0000	1.0000
JC69I	36	-1252.5184	2585.1836	0.0000	1.0000
JC69IG	37	-1251.9256	2586.4769	0.0000	1.0000
F81	38	-1253.4516	2592.0231	0.0000	1.0000
JC69	35	-1267.5714	2612.8258	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1202.5009	2485.0017	0.4917	0.4917
HKYI	40	-1203.1001	2486.2003	0.2701	0.7618
HKYIG	41	-1202.4915	2486.9831	0.1826	0.9444
GTRG	44	-1201.3343	2490.6687	0.0289	0.9733
GTRI	44	-1201.9327	2491.8653	0.0159	0.9892
GTRIG	45	-1201.3184	2492.6368	0.0108	1.0000
K2PG	37	-1219.8705	2513.7410	0.0000	1.0000
HKY	39	-1218.5382	2515.0764	0.0000	1.0000
K2PI	37	-1220.5408	2515.0817	0.0000	1.0000
K2PIG	38	-1219.8596	2515.7192	0.0000	1.0000
SYMG	41	-1219.4257	2520.8513	0.0000	1.0000
GTR	43	-1217.4507	2520.9015	0.0000	1.0000
SYMI	41	-1220.1296	2522.2592	0.0000	1.0000
SYMIG	42	-1219.4123	2522.8245	0.0000	1.0000
K2P	36	-1236.1478	2544.2957	0.0000	1.0000
SYM	40	-1235.7947	2551.5894	0.0000	1.0000
F81G	39	-1238.0133	2554.0267	0.0000	1.0000
F81I	39	-1238.5554	2555.1107	0.0000	1.0000
F81IG	40	-1238.0104	2556.0209	0.0000	1.0000
JC69G	36	-1251.9287	2575.8573	0.0000	1.0000
JC69I	36	-1252.5184	2577.0368	0.0000	1.0000
JC69IG	37	-1251.9256	2577.8511	0.0000	1.0000
F81	38	-1253.4516	2582.9031	0.0000	1.0000
JC69	35	-1267.5714	2605.1428	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1202.5009	2640.8879	0.6240	0.6240
HKYI	40	-1203.1001	2642.0865	0.3427	0.9668
HKYIG	41	-1202.4915	2646.7664	0.0330	0.9998
K2PG	37	-1219.8705	2657.9357	0.0001	0.9999
K2PI	37	-1220.5408	2659.2764	0.0001	1.0000
GTRG	44	-1201.3343	2662.1434	0.0000	1.0000
GTRI	44	-1201.9327	2663.3401	0.0000	1.0000
K2PIG	38	-1219.8596	2663.8110	0.0000	1.0000
HKY	39	-1218.5382	2667.0654	0.0000	1.0000
GTRIG	45	-1201.3184	2668.0087	0.0000	1.0000
SYMG	41	-1219.4257	2680.6346	0.0000	1.0000
SYMI	41	-1220.1296	2682.0425	0.0000	1.0000
K2P	36	-1236.1478	2684.5932	0.0000	1.0000
SYMIG	42	-1219.4123	2686.5050	0.0000	1.0000
GTR	43	-1217.4507	2688.4791	0.0000	1.0000
F81G	39	-1238.0133	2706.0157	0.0000	1.0000
F81I	39	-1238.5554	2707.0997	0.0000	1.0000
SYM	40	-1235.7947	2707.4755	0.0000	1.0000
F81IG	40	-1238.0104	2711.9071	0.0000	1.0000
JC69G	36	-1251.9287	2716.1549	0.0000	1.0000
JC69I	36	-1252.5184	2717.3343	0.0000	1.0000
JC69IG	37	-1251.9256	2722.0458	0.0000	1.0000
F81	38	-1253.4516	2730.9950	0.0000	1.0000
JC69	35	-1267.5714	2741.5432	0.0000	1.0000



To specify default values for best AIC, AICc, or BIC models in MrBayes:

[Mrbayes block for the best AIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9731.phylip = 1 - 364;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9731.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 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);
END;


[Mrbayes block for the best AICc model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9731.phylip = 1 - 364;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9731.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 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);
END;


[Mrbayes block for the best BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9731.phylip = 1 - 364;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_9731.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 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);
END;


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End of Output

