
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:20 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/chr17_2952.phylip" (19 taxa, 565 characters)

Minimum AIC  model: SYMI
Minimum AICc model: SYMI
Minimum BIC  model: K2PI


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
SYMI	41	-1503.4241	3095.4333	0.4941	0.4941
SYMG	41	-1504.1204	3096.8258	0.2463	0.7405
K2PI	37	-1509.8346	3099.0051	0.0828	0.8233
SYMIG	42	-1504.1199	3099.1594	0.0767	0.9000
K2PG	37	-1510.4271	3100.1900	0.0458	0.9458
GTRI	44	-1503.1267	3101.8689	0.0198	0.9656
K2PIG	38	-1510.5023	3102.6397	0.0135	0.9790
GTRG	44	-1503.8173	3103.2499	0.0099	0.9890
HKYI	40	-1509.2223	3104.7042	0.0048	0.9938
GTRIG	45	-1503.9209	3105.8187	0.0027	0.9965
HKYG	40	-1509.8011	3105.8617	0.0027	0.9992
HKYIG	41	-1509.8730	3108.3312	0.0008	1.0000
SYM	40	-1514.6605	3115.5806	0.0000	1.0000
K2P	36	-1520.3329	3117.7113	0.0000	1.0000
GTR	43	-1514.2426	3121.7481	0.0000	1.0000
HKY	39	-1519.6456	3123.2342	0.0000	1.0000
JC69I	36	-1535.6069	3148.2593	0.0000	1.0000
JC69G	36	-1536.0734	3149.1923	0.0000	1.0000
JC69IG	37	-1536.1243	3151.5844	0.0000	1.0000
F81I	39	-1534.8499	3153.6427	0.0000	1.0000
F81G	39	-1535.1946	3154.3320	0.0000	1.0000
F81IG	40	-1535.1870	3156.6334	0.0000	1.0000
JC69	35	-1545.3001	3165.3638	0.0000	1.0000
F81	38	-1544.5479	3170.7309	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMI	41	-1503.4241	3088.8483	0.5090	0.5090
SYMG	41	-1504.1204	3090.2407	0.2537	0.7628
SYMIG	42	-1504.1199	3092.2399	0.0934	0.8561
K2PI	37	-1509.8346	3093.6693	0.0457	0.9018
GTRI	44	-1503.1267	3094.2535	0.0341	0.9360
K2PG	37	-1510.4271	3094.8541	0.0253	0.9612
GTRG	44	-1503.8173	3095.6345	0.0171	0.9783
K2PIG	38	-1510.5023	3097.0047	0.0086	0.9869
GTRIG	45	-1503.9209	3097.8419	0.0057	0.9926
HKYI	40	-1509.2223	3098.4447	0.0042	0.9968
HKYG	40	-1509.8011	3099.6021	0.0024	0.9992
HKYIG	41	-1509.8730	3101.7461	0.0008	1.0000
SYM	40	-1514.6605	3109.3210	0.0000	1.0000
K2P	36	-1520.3329	3112.6659	0.0000	1.0000
GTR	43	-1514.2426	3114.4852	0.0000	1.0000
HKY	39	-1519.6456	3117.2913	0.0000	1.0000
JC69I	36	-1535.6069	3143.2138	0.0000	1.0000
JC69G	36	-1536.0734	3144.1468	0.0000	1.0000
JC69IG	37	-1536.1243	3146.2485	0.0000	1.0000
F81I	39	-1534.8499	3147.6998	0.0000	1.0000
F81G	39	-1535.1946	3148.3892	0.0000	1.0000
F81IG	40	-1535.1870	3150.3739	0.0000	1.0000
JC69	35	-1545.3001	3160.6001	0.0000	1.0000
F81	38	-1544.5479	3165.0959	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2PI	37	-1509.8346	3254.1318	0.6336	0.6336
K2PG	37	-1510.4271	3255.3167	0.3504	0.9839
K2PIG	38	-1510.5023	3261.8041	0.0137	0.9976
SYMI	41	-1503.4241	3266.6581	0.0012	0.9988
SYMG	41	-1504.1204	3268.0506	0.0006	0.9994
K2P	36	-1520.3329	3268.7916	0.0004	0.9998
HKYI	40	-1509.2223	3271.9177	0.0001	0.9999
HKYG	40	-1509.8011	3273.0752	0.0000	1.0000
SYMIG	42	-1504.1199	3274.3866	0.0000	1.0000
HKYIG	41	-1509.8730	3279.5560	0.0000	1.0000
SYM	40	-1514.6605	3282.7941	0.0000	1.0000
GTRI	44	-1503.1267	3285.0738	0.0000	1.0000
HKY	39	-1519.6456	3286.4275	0.0000	1.0000
GTRG	44	-1503.8173	3286.4549	0.0000	1.0000
GTRIG	45	-1503.9209	3292.9990	0.0000	1.0000
JC69I	36	-1535.6069	3299.3395	0.0000	1.0000
JC69G	36	-1536.0734	3300.2725	0.0000	1.0000
GTR	43	-1514.2426	3300.9687	0.0000	1.0000
JC69IG	37	-1536.1243	3306.7111	0.0000	1.0000
JC69	35	-1545.3001	3312.3890	0.0000	1.0000
F81I	39	-1534.8499	3316.8360	0.0000	1.0000
F81G	39	-1535.1946	3317.5254	0.0000	1.0000
F81IG	40	-1535.1870	3323.8469	0.0000	1.0000
F81	38	-1544.5479	3329.8953	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2952.phylip = 1 - 565;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2952.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Fixed(Equal) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2952.phylip = 1 - 565;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2952.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=6 rates=propinv;
 Prset applyto=(1) revmatpr=Dirichlet(1.0,1.0,1.0,1.0,1.0,1.0) statefreqpr=Fixed(Equal) pinvarpr=Uniform(0.0,1.0);
END;


[Mrbayes block for the best BIC model (K2PI)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2952.phylip = 1 - 565;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_2952.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

