
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
12:49 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_1379.phylip" (19 taxa, 333 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
Minimum BIC  model: K2PG


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
SYMG	41	-1167.5568	2428.9487	0.4723	0.4723
GTRG	44	-1164.5655	2430.8810	0.1797	0.6520
SYMIG	42	-1167.3785	2431.2121	0.1523	0.8043
K2PG	37	-1174.7699	2433.0720	0.0601	0.8644
GTRIG	45	-1164.5866	2433.5983	0.0462	0.9106
K2PIG	38	-1174.0663	2434.2143	0.0339	0.9446
SYMI	41	-1170.3061	2434.4473	0.0302	0.9748
HKYIG	41	-1171.4214	2436.6779	0.0099	0.9847
GTRI	44	-1167.6164	2436.9829	0.0085	0.9932
HKYG	40	-1173.7043	2438.6415	0.0037	0.9969
K2PI	37	-1177.7975	2439.1273	0.0029	0.9998
HKYI	40	-1176.6536	2444.5401	0.0002	1.0000
JC69IG	37	-1188.2096	2459.9513	0.0000	1.0000
JC69G	36	-1190.1916	2461.3832	0.0000	1.0000
F81G	39	-1188.2795	2465.2075	0.0000	1.0000
F81IG	40	-1187.1550	2465.5429	0.0000	1.0000
JC69I	36	-1193.0347	2467.0694	0.0000	1.0000
F81I	39	-1190.8693	2470.3871	0.0000	1.0000
SYM	40	-1211.5027	2514.2382	0.0000	1.0000
GTR	43	-1208.6442	2516.3819	0.0000	1.0000
K2P	36	-1218.0405	2517.0809	0.0000	1.0000
HKY	39	-1216.9641	2522.5766	0.0000	1.0000
JC69	35	-1232.9516	2544.3881	0.0000	1.0000
F81	38	-1231.2525	2548.5866	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-1167.5568	2417.1137	0.3335	0.3335
GTRG	44	-1164.5655	2417.1310	0.3307	0.6642
SYMIG	42	-1167.3785	2418.7569	0.1467	0.8108
GTRIG	45	-1164.5866	2419.1732	0.1191	0.9299
SYMI	41	-1170.3061	2422.6123	0.0213	0.9513
GTRI	44	-1167.6164	2423.2329	0.0156	0.9669
K2PG	37	-1174.7699	2423.5398	0.0134	0.9803
K2PIG	38	-1174.0663	2424.1326	0.0100	0.9903
HKYIG	41	-1171.4214	2424.8428	0.0070	0.9973
HKYG	40	-1173.7043	2427.4086	0.0019	0.9992
K2PI	37	-1177.7975	2429.5951	0.0006	0.9999
HKYI	40	-1176.6536	2433.3073	0.0001	1.0000
JC69IG	37	-1188.2096	2450.4191	0.0000	1.0000
JC69G	36	-1190.1916	2452.3832	0.0000	1.0000
F81IG	40	-1187.1550	2454.3100	0.0000	1.0000
F81G	39	-1188.2795	2454.5590	0.0000	1.0000
JC69I	36	-1193.0347	2458.0694	0.0000	1.0000
F81I	39	-1190.8693	2459.7386	0.0000	1.0000
SYM	40	-1211.5027	2503.0053	0.0000	1.0000
GTR	43	-1208.6442	2503.2885	0.0000	1.0000
K2P	36	-1218.0405	2508.0809	0.0000	1.0000
HKY	39	-1216.9641	2511.9281	0.0000	1.0000
JC69	35	-1232.9516	2535.9033	0.0000	1.0000
F81	38	-1231.2525	2538.5050	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PG	37	-1174.7699	2564.4411	0.8519	0.8519
K2PIG	38	-1174.0663	2568.8421	0.0944	0.9463
K2PI	37	-1177.7975	2570.4963	0.0413	0.9875
SYMG	41	-1167.5568	2573.2475	0.0104	0.9980
SYMIG	42	-1167.3785	2578.6989	0.0007	0.9986
SYMI	41	-1170.3061	2578.7461	0.0007	0.9993
HKYG	40	-1173.7043	2579.7343	0.0004	0.9997
HKYIG	41	-1171.4214	2580.9766	0.0002	0.9999
GTRG	44	-1164.5655	2584.6892	0.0000	1.0000
HKYI	40	-1176.6536	2585.6330	0.0000	1.0000
JC69G	36	-1190.1916	2589.4763	0.0000	1.0000
GTRIG	45	-1164.5866	2590.5396	0.0000	1.0000
GTRI	44	-1167.6164	2590.7911	0.0000	1.0000
JC69IG	37	-1188.2096	2591.3204	0.0000	1.0000
JC69I	36	-1193.0347	2595.1625	0.0000	1.0000
F81G	39	-1188.2795	2603.0766	0.0000	1.0000
F81IG	40	-1187.1550	2606.6357	0.0000	1.0000
F81I	39	-1190.8693	2608.2562	0.0000	1.0000
K2P	36	-1218.0405	2645.1740	0.0000	1.0000
SYM	40	-1211.5027	2655.3310	0.0000	1.0000
HKY	39	-1216.9641	2660.4457	0.0000	1.0000
GTR	43	-1208.6442	2667.0386	0.0000	1.0000
JC69	35	-1232.9516	2669.1882	0.0000	1.0000
F81	38	-1231.2525	2683.2144	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1379.phylip = 1 - 333;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1379.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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1379.phylip = 1 - 333;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1379.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=Fixed(Equal);
END;


[Mrbayes block for the best BIC model (K2PG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1379.phylip = 1 - 333;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr7_1379.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=gamma;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) shapepr=Uniform(0.1,50.0);
END;


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End of Output

