
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:45 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_18733.phylip" (19 taxa, 365 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	-1176.5635	2443.2504	0.4960	0.4960
HKYI	40	-1177.4219	2444.9672	0.2102	0.7062
HKYIG	41	-1176.3646	2445.3917	0.1700	0.8762
GTRG	44	-1173.4050	2447.1850	0.0694	0.9456
GTRI	44	-1174.2260	2448.8270	0.0305	0.9761
GTRIG	45	-1173.1849	2449.3479	0.0235	0.9996
K2PG	37	-1188.0371	2458.6735	0.0002	0.9998
K2PIG	38	-1187.8237	2460.7394	0.0001	0.9999
K2PI	37	-1189.1886	2460.9765	0.0001	1.0000
SYMG	41	-1185.4907	2463.6440	0.0000	1.0000
SYMIG	42	-1185.2868	2465.7910	0.0000	1.0000
SYMI	41	-1186.7140	2466.0905	0.0000	1.0000
HKY	39	-1193.9130	2475.4259	0.0000	1.0000
GTR	43	-1190.5343	2478.8568	0.0000	1.0000
K2P	36	-1205.7598	2491.6415	0.0000	1.0000
SYM	40	-1202.2278	2494.5791	0.0000	1.0000
F81G	39	-1205.5565	2498.7130	0.0000	1.0000
F81I	39	-1206.5505	2500.7010	0.0000	1.0000
F81IG	40	-1205.4237	2500.9710	0.0000	1.0000
JC69G	36	-1215.6570	2511.4360	0.0000	1.0000
JC69I	36	-1216.6231	2513.3682	0.0000	1.0000
JC69IG	37	-1215.5362	2513.6718	0.0000	1.0000
F81	38	-1222.6443	2530.3807	0.0000	1.0000
JC69	35	-1232.4167	2542.4930	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYG	40	-1176.5635	2433.1269	0.3715	0.3715
HKYIG	41	-1176.3646	2434.7292	0.1668	0.5383
GTRG	44	-1173.4050	2434.8100	0.1602	0.6985
HKYI	40	-1177.4219	2434.8437	0.1575	0.8559
GTRIG	45	-1173.1849	2436.3698	0.0734	0.9294
GTRI	44	-1174.2260	2436.4520	0.0705	0.9998
K2PG	37	-1188.0371	2450.0741	0.0001	0.9999
K2PIG	38	-1187.8237	2451.6473	0.0000	0.9999
K2PI	37	-1189.1886	2452.3771	0.0000	1.0000
SYMG	41	-1185.4907	2452.9814	0.0000	1.0000
SYMIG	42	-1185.2868	2454.5736	0.0000	1.0000
SYMI	41	-1186.7140	2455.4279	0.0000	1.0000
HKY	39	-1193.9130	2465.8259	0.0000	1.0000
GTR	43	-1190.5343	2467.0686	0.0000	1.0000
K2P	36	-1205.7598	2483.5195	0.0000	1.0000
SYM	40	-1202.2278	2484.4556	0.0000	1.0000
F81G	39	-1205.5565	2489.1130	0.0000	1.0000
F81IG	40	-1205.4237	2490.8475	0.0000	1.0000
F81I	39	-1206.5505	2491.1010	0.0000	1.0000
JC69G	36	-1215.6570	2503.3140	0.0000	1.0000
JC69IG	37	-1215.5362	2505.0724	0.0000	1.0000
JC69I	36	-1216.6231	2505.2463	0.0000	1.0000
F81	38	-1222.6443	2521.2886	0.0000	1.0000
JC69	35	-1232.4167	2534.8334	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1176.5635	2589.1228	0.6297	0.6297
HKYI	40	-1177.4219	2590.8396	0.2669	0.8965
K2PG	37	-1188.0371	2594.3703	0.0457	0.9422
HKYIG	41	-1176.3646	2594.6250	0.0402	0.9824
K2PI	37	-1189.1886	2596.6733	0.0144	0.9969
K2PIG	38	-1187.8237	2599.8434	0.0030	0.9998
GTRG	44	-1173.4050	2606.4055	0.0001	0.9999
GTRI	44	-1174.2260	2608.0475	0.0000	1.0000
GTRIG	45	-1173.1849	2611.8652	0.0000	1.0000
SYMG	41	-1185.4907	2612.8772	0.0000	1.0000
SYMI	41	-1186.7140	2615.3237	0.0000	1.0000
HKY	39	-1193.9130	2617.9219	0.0000	1.0000
SYMIG	42	-1185.2868	2618.3693	0.0000	1.0000
K2P	36	-1205.7598	2623.9158	0.0000	1.0000
GTR	43	-1190.5343	2634.7642	0.0000	1.0000
SYM	40	-1202.2278	2640.4515	0.0000	1.0000
F81G	39	-1205.5565	2641.2090	0.0000	1.0000
F81I	39	-1206.5505	2643.1970	0.0000	1.0000
JC69G	36	-1215.6570	2643.7103	0.0000	1.0000
JC69I	36	-1216.6231	2645.6426	0.0000	1.0000
F81IG	40	-1205.4237	2646.8434	0.0000	1.0000
JC69IG	37	-1215.5362	2649.3686	0.0000	1.0000
F81	38	-1222.6443	2669.4847	0.0000	1.0000
JC69	35	-1232.4167	2671.3298	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/chr2_18733.phylip = 1 - 365;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18733.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/chr2_18733.phylip = 1 - 365;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18733.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/chr2_18733.phylip = 1 - 365;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr2_18733.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

