
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:55 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/chr2_21284.phylip" (19 taxa, 533 characters)

Minimum AIC  model: GTRG
Minimum AICc model: GTRG
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
GTRG	44	-1413.2136	2922.5420	0.3953	0.3953
GTRI	44	-1413.9929	2924.1006	0.1813	0.5767
HKYG	40	-1419.0502	2924.7670	0.1300	0.7066
GTRIG	45	-1413.2144	2924.9297	0.1198	0.8264
HKYI	40	-1419.6569	2925.9805	0.0708	0.8973
GTR	43	-1416.4704	2926.6790	0.0500	0.9472
HKYIG	41	-1419.0602	2927.1347	0.0398	0.9870
HKY	39	-1422.5219	2929.3723	0.0130	1.0000
F81G	39	-1439.6919	2963.7125	0.0000	1.0000
F81I	39	-1440.2554	2964.8395	0.0000	1.0000
F81IG	40	-1439.7054	2966.0774	0.0000	1.0000
F81	38	-1443.1660	2968.3319	0.0000	1.0000
K2PG	37	-1446.3233	2972.3275	0.0000	1.0000
K2PI	37	-1446.7901	2973.2610	0.0000	1.0000
K2PIG	38	-1446.3411	2974.6822	0.0000	1.0000
SYMG	41	-1444.1392	2977.2927	0.0000	1.0000
K2P	36	-1450.3406	2978.0522	0.0000	1.0000
SYMI	41	-1444.6337	2978.2817	0.0000	1.0000
SYMIG	42	-1444.1563	2979.6841	0.0000	1.0000
SYM	40	-1447.8344	2982.3355	0.0000	1.0000
JC69G	36	-1463.8817	3005.1343	0.0000	1.0000
JC69I	36	-1464.3835	3006.1380	0.0000	1.0000
JC69IG	37	-1463.8983	3007.4775	0.0000	1.0000
JC69	35	-1467.7287	3010.5278	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1413.2136	2914.4273	0.4447	0.4447
GTRI	44	-1413.9929	2915.9858	0.2040	0.6487
GTRIG	45	-1413.2144	2916.4287	0.1635	0.8121
HKYG	40	-1419.0502	2918.1003	0.0709	0.8830
GTR	43	-1416.4704	2918.9407	0.0466	0.9296
HKYI	40	-1419.6569	2919.3138	0.0386	0.9682
HKYIG	41	-1419.0602	2920.1204	0.0258	0.9940
HKY	39	-1422.5219	2923.0437	0.0060	1.0000
F81G	39	-1439.6919	2957.3839	0.0000	1.0000
F81I	39	-1440.2554	2958.5109	0.0000	1.0000
F81IG	40	-1439.7054	2959.4108	0.0000	1.0000
F81	38	-1443.1660	2962.3319	0.0000	1.0000
K2PG	37	-1446.3233	2966.6467	0.0000	1.0000
K2PI	37	-1446.7901	2967.5802	0.0000	1.0000
K2PIG	38	-1446.3411	2968.6822	0.0000	1.0000
SYMG	41	-1444.1392	2970.2784	0.0000	1.0000
SYMI	41	-1444.6337	2971.2675	0.0000	1.0000
SYMIG	42	-1444.1563	2972.3127	0.0000	1.0000
K2P	36	-1450.3406	2972.6812	0.0000	1.0000
SYM	40	-1447.8344	2975.6688	0.0000	1.0000
JC69G	36	-1463.8817	2999.7633	0.0000	1.0000
JC69I	36	-1464.3835	3000.7671	0.0000	1.0000
JC69IG	37	-1463.8983	3001.7967	0.0000	1.0000
JC69	35	-1467.7287	3005.4574	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1419.0502	3089.2412	0.4333	0.4333
HKY	39	-1422.5219	3089.9061	0.3107	0.7440
HKYI	40	-1419.6569	3090.4547	0.2362	0.9802
HKYIG	41	-1419.0602	3095.5398	0.0186	0.9988
GTRG	44	-1413.2136	3102.6822	0.0005	0.9993
GTR	43	-1416.4704	3102.9172	0.0005	0.9997
GTRI	44	-1413.9929	3104.2408	0.0002	1.0000
GTRIG	45	-1413.2144	3108.9622	0.0000	1.0000
F81G	39	-1439.6919	3124.2462	0.0000	1.0000
F81	38	-1443.1660	3124.9158	0.0000	1.0000
K2PG	37	-1446.3233	3124.9520	0.0000	1.0000
F81I	39	-1440.2554	3125.3732	0.0000	1.0000
K2PI	37	-1446.7901	3125.8855	0.0000	1.0000
K2P	36	-1450.3406	3126.7080	0.0000	1.0000
F81IG	40	-1439.7054	3130.5516	0.0000	1.0000
K2PIG	38	-1446.3411	3131.2660	0.0000	1.0000
SYMG	41	-1444.1392	3145.6978	0.0000	1.0000
SYMI	41	-1444.6337	3146.6868	0.0000	1.0000
SYM	40	-1447.8344	3146.8097	0.0000	1.0000
SYMIG	42	-1444.1563	3152.0106	0.0000	1.0000
JC69G	36	-1463.8817	3153.7901	0.0000	1.0000
JC69I	36	-1464.3835	3154.7939	0.0000	1.0000
JC69	35	-1467.7287	3155.2056	0.0000	1.0000
JC69IG	37	-1463.8983	3160.1020	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/chr2_21284.phylip = 1 - 533;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21284.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 (GTRG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21284.phylip = 1 - 533;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21284.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 BIC model (HKYG)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21284.phylip = 1 - 533;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_21284.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

