
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:04 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/chr7_11469.phylip" (19 taxa, 432 characters)

Minimum AIC  model: GTRG
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	-1166.8893	2422.1673	0.3246	0.3246
HKYI	40	-1167.1859	2422.7605	0.2413	0.5658
GTRG	44	-1162.6310	2423.4946	0.1671	0.7330
GTRI	44	-1163.0373	2424.3072	0.1113	0.8443
HKYIG	41	-1166.8913	2424.6134	0.0955	0.9398
GTRIG	45	-1162.6315	2425.9883	0.0480	0.9879
HKY	39	-1171.6660	2429.2912	0.0092	0.9971
GTR	43	-1167.9216	2431.5958	0.0029	1.0000
F81G	39	-1181.5501	2449.0594	0.0000	1.0000
F81I	39	-1181.9122	2449.7836	0.0000	1.0000
F81IG	40	-1181.5612	2451.5112	0.0000	1.0000
F81	38	-1185.8895	2455.3210	0.0000	1.0000
K2PG	37	-1192.3259	2465.7888	0.0000	1.0000
K2PI	37	-1192.6031	2466.3433	0.0000	1.0000
K2PIG	38	-1192.3307	2468.2034	0.0000	1.0000
SYMG	41	-1189.5863	2470.0034	0.0000	1.0000
SYMI	41	-1189.8532	2470.5372	0.0000	1.0000
SYMIG	42	-1189.5873	2472.4599	0.0000	1.0000
K2P	36	-1197.2479	2473.2401	0.0000	1.0000
SYM	40	-1194.8218	2478.0323	0.0000	1.0000
JC69G	36	-1205.0272	2488.7988	0.0000	1.0000
JC69I	36	-1205.3723	2489.4890	0.0000	1.0000
JC69IG	37	-1205.0358	2491.2086	0.0000	1.0000
JC69	35	-1209.6101	2495.5838	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1162.6310	2413.2620	0.2706	0.2706
HKYG	40	-1166.8893	2413.7785	0.2090	0.4796
GTRI	44	-1163.0373	2414.0747	0.1803	0.6599
HKYI	40	-1167.1859	2414.3718	0.1554	0.8153
GTRIG	45	-1162.6315	2415.2629	0.0995	0.9148
HKYIG	41	-1166.8913	2415.7826	0.0767	0.9915
HKY	39	-1171.6660	2421.3320	0.0048	0.9963
GTR	43	-1167.9216	2421.8432	0.0037	1.0000
F81G	39	-1181.5501	2441.1002	0.0000	1.0000
F81I	39	-1181.9122	2441.8244	0.0000	1.0000
F81IG	40	-1181.5612	2443.1225	0.0000	1.0000
F81	38	-1185.8895	2447.7790	0.0000	1.0000
K2PG	37	-1192.3259	2458.6517	0.0000	1.0000
K2PI	37	-1192.6031	2459.2063	0.0000	1.0000
K2PIG	38	-1192.3307	2460.6614	0.0000	1.0000
SYMG	41	-1189.5863	2461.1727	0.0000	1.0000
SYMI	41	-1189.8532	2461.7064	0.0000	1.0000
SYMIG	42	-1189.5873	2463.1746	0.0000	1.0000
K2P	36	-1197.2479	2466.4958	0.0000	1.0000
SYM	40	-1194.8218	2469.6435	0.0000	1.0000
JC69G	36	-1205.0272	2482.0545	0.0000	1.0000
JC69I	36	-1205.3723	2482.7447	0.0000	1.0000
JC69IG	37	-1205.0358	2484.0716	0.0000	1.0000
JC69	35	-1209.6101	2489.2201	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1166.8893	2576.5156	0.5084	0.5084
HKYI	40	-1167.1859	2577.1088	0.3779	0.8862
HKY	39	-1171.6660	2580.0006	0.0890	0.9752
HKYIG	41	-1166.8913	2582.5880	0.0244	0.9996
GTRG	44	-1162.6310	2592.2727	0.0002	0.9998
GTRI	44	-1163.0373	2593.0854	0.0001	1.0000
GTR	43	-1167.9216	2596.7855	0.0000	1.0000
GTRIG	45	-1162.6315	2598.3421	0.0000	1.0000
F81G	39	-1181.5501	2599.7688	0.0000	1.0000
F81I	39	-1181.9122	2600.4930	0.0000	1.0000
F81	38	-1185.8895	2602.3792	0.0000	1.0000
F81IG	40	-1181.5612	2605.8595	0.0000	1.0000
K2PG	37	-1192.3259	2609.1835	0.0000	1.0000
K2PI	37	-1192.6031	2609.7380	0.0000	1.0000
K2P	36	-1197.2479	2612.9591	0.0000	1.0000
K2PIG	38	-1192.3307	2615.2616	0.0000	1.0000
SYMG	41	-1189.5863	2627.9781	0.0000	1.0000
SYMI	41	-1189.8532	2628.5118	0.0000	1.0000
JC69G	36	-1205.0272	2628.5178	0.0000	1.0000
JC69I	36	-1205.3723	2629.2080	0.0000	1.0000
JC69	35	-1209.6101	2631.6150	0.0000	1.0000
SYM	40	-1194.8218	2632.3806	0.0000	1.0000
SYMIG	42	-1189.5873	2634.0485	0.0000	1.0000
JC69IG	37	-1205.0358	2634.6033	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11469.phylip = 1 - 432;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11469.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=gamma;
 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) 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/chr7_11469.phylip = 1 - 432;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11469.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/chr7_11469.phylip = 1 - 432;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_11469.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

