
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:13 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_22050.phylip" (19 taxa, 304 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	-1094.3811	2292.0518	0.5768	0.5768
GTRIG	45	-1094.3487	2294.7439	0.1501	0.7269
HKYG	40	-1101.1964	2294.8643	0.1413	0.8682
GTRI	44	-1096.4300	2296.1496	0.0743	0.9425
HKYIG	41	-1101.1733	2297.4915	0.0380	0.9805
HKYI	40	-1103.1836	2298.8388	0.0194	0.9999
GTR	43	-1104.9013	2310.3564	0.0001	1.0000
HKY	39	-1111.2069	2312.2319	0.0000	1.0000
K2PG	37	-1119.6477	2323.8667	0.0000	1.0000
SYMG	41	-1114.8288	2324.8026	0.0000	1.0000
K2PIG	38	-1119.6155	2326.4159	0.0000	1.0000
SYMIG	42	-1114.7891	2327.4173	0.0000	1.0000
K2PI	37	-1121.5415	2327.6544	0.0000	1.0000
SYMI	41	-1116.5790	2328.3030	0.0000	1.0000
F81G	39	-1124.5569	2338.9320	0.0000	1.0000
F81IG	40	-1124.5271	2341.5257	0.0000	1.0000
K2P	36	-1130.2889	2342.5553	0.0000	1.0000
F81I	39	-1126.6803	2343.1787	0.0000	1.0000
SYM	40	-1125.8069	2344.0853	0.0000	1.0000
F81	38	-1134.7279	2356.6407	0.0000	1.0000
JC69G	36	-1140.3575	2362.6926	0.0000	1.0000
JC69IG	37	-1140.3265	2365.2244	0.0000	1.0000
JC69I	36	-1142.3502	2366.6780	0.0000	1.0000
JC69	35	-1150.8528	2381.1086	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1094.3811	2276.7622	0.6252	0.6252
GTRIG	45	-1094.3487	2278.6973	0.2376	0.8627
GTRI	44	-1096.4300	2280.8600	0.0806	0.9433
HKYG	40	-1101.1964	2282.3928	0.0374	0.9807
HKYIG	41	-1101.1733	2284.3465	0.0141	0.9948
HKYI	40	-1103.1836	2286.3673	0.0051	0.9999
GTR	43	-1104.9013	2295.8025	0.0000	1.0000
HKY	39	-1111.2069	2300.4137	0.0000	1.0000
SYMG	41	-1114.8288	2311.6576	0.0000	1.0000
K2PG	37	-1119.6477	2313.2953	0.0000	1.0000
SYMIG	42	-1114.7891	2313.5782	0.0000	1.0000
SYMI	41	-1116.5790	2315.1580	0.0000	1.0000
K2PIG	38	-1119.6155	2315.2310	0.0000	1.0000
K2PI	37	-1121.5415	2317.0829	0.0000	1.0000
F81G	39	-1124.5569	2327.1138	0.0000	1.0000
F81IG	40	-1124.5271	2329.0542	0.0000	1.0000
F81I	39	-1126.6803	2331.3606	0.0000	1.0000
SYM	40	-1125.8069	2331.6138	0.0000	1.0000
K2P	36	-1130.2889	2332.5778	0.0000	1.0000
F81	38	-1134.7279	2345.4558	0.0000	1.0000
JC69G	36	-1140.3575	2352.7151	0.0000	1.0000
JC69IG	37	-1140.3265	2354.6530	0.0000	1.0000
JC69I	36	-1142.3502	2356.7004	0.0000	1.0000
JC69	35	-1150.8528	2371.7056	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1101.1964	2431.0739	0.8276	0.8276
HKYI	40	-1103.1836	2435.0484	0.1134	0.9410
HKYIG	41	-1101.1733	2436.7446	0.0486	0.9896
GTRG	44	-1094.3811	2440.3114	0.0082	0.9978
GTRI	44	-1096.4300	2444.4093	0.0011	0.9988
HKY	39	-1111.2069	2445.3778	0.0006	0.9995
GTRIG	45	-1094.3487	2445.9636	0.0005	0.9999
K2PG	37	-1119.6477	2450.8253	0.0000	1.0000
K2PI	37	-1121.5415	2454.6130	0.0000	1.0000
GTR	43	-1104.9013	2455.6347	0.0000	1.0000
K2PIG	38	-1119.6155	2456.4781	0.0000	1.0000
SYMG	41	-1114.8288	2464.0557	0.0000	1.0000
K2P	36	-1130.2889	2466.3908	0.0000	1.0000
SYMI	41	-1116.5790	2467.5561	0.0000	1.0000
SYMIG	42	-1114.7891	2469.6934	0.0000	1.0000
F81G	39	-1124.5569	2472.0779	0.0000	1.0000
F81I	39	-1126.6803	2476.3246	0.0000	1.0000
F81IG	40	-1124.5271	2477.7353	0.0000	1.0000
SYM	40	-1125.8069	2480.2949	0.0000	1.0000
JC69G	36	-1140.3575	2486.5281	0.0000	1.0000
F81	38	-1134.7279	2486.7029	0.0000	1.0000
JC69I	36	-1142.3502	2490.5134	0.0000	1.0000
JC69IG	37	-1140.3265	2492.1830	0.0000	1.0000
JC69	35	-1150.8528	2501.8016	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_22050.phylip = 1 - 304;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22050.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_22050.phylip = 1 - 304;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22050.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_22050.phylip = 1 - 304;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_22050.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

