
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
13:06 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/chr9_7138.phylip" (19 taxa, 446 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	-1492.2560	3082.3873	0.6002	0.6002
GTRIG	45	-1492.2495	3084.8490	0.1753	0.7755
GTRI	44	-1493.6431	3085.1616	0.1499	0.9254
HKYG	40	-1499.8277	3087.7542	0.0410	0.9664
HKYI	40	-1500.4808	3089.0605	0.0213	0.9878
HKYIG	41	-1499.8262	3090.1772	0.0122	1.0000
GTR	43	-1507.7068	3110.8265	0.0000	1.0000
HKY	39	-1514.3373	3114.3593	0.0000	1.0000
K2PG	37	-1522.0802	3125.0525	0.0000	1.0000
K2PI	37	-1522.2472	3125.3865	0.0000	1.0000
K2PIG	38	-1522.0072	3127.2969	0.0000	1.0000
SYMG	41	-1520.7719	3132.0685	0.0000	1.0000
SYMI	41	-1521.2577	3133.0402	0.0000	1.0000
SYMIG	42	-1520.6817	3134.3261	0.0000	1.0000
K2P	36	-1536.6618	3151.8370	0.0000	1.0000
SYM	40	-1536.8572	3161.8132	0.0000	1.0000
F81G	39	-1544.2776	3174.2399	0.0000	1.0000
F81I	39	-1544.4728	3174.6303	0.0000	1.0000
F81IG	40	-1544.2293	3176.5573	0.0000	1.0000
F81	38	-1557.4667	3198.2160	0.0000	1.0000
JC69I	36	-1563.1148	3204.7430	0.0000	1.0000
JC69G	36	-1563.2840	3205.0814	0.0000	1.0000
JC69IG	37	-1563.0313	3206.9548	0.0000	1.0000
JC69	35	-1577.5927	3231.3317	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
GTRG	44	-1492.2560	3072.5120	0.5977	0.5977
GTRIG	45	-1492.2495	3074.4990	0.2213	0.8190
GTRI	44	-1493.6431	3075.2863	0.1493	0.9683
HKYG	40	-1499.8277	3079.6554	0.0168	0.9851
HKYI	40	-1500.4808	3080.9617	0.0087	0.9938
HKYIG	41	-1499.8262	3081.6524	0.0062	1.0000
GTR	43	-1507.7068	3101.4136	0.0000	1.0000
HKY	39	-1514.3373	3106.6746	0.0000	1.0000
K2PG	37	-1522.0802	3118.1603	0.0000	1.0000
K2PI	37	-1522.2472	3118.4943	0.0000	1.0000
K2PIG	38	-1522.0072	3120.0143	0.0000	1.0000
SYMG	41	-1520.7719	3123.5437	0.0000	1.0000
SYMI	41	-1521.2577	3124.5154	0.0000	1.0000
SYMIG	42	-1520.6817	3125.3633	0.0000	1.0000
K2P	36	-1536.6618	3145.3236	0.0000	1.0000
SYM	40	-1536.8572	3153.7145	0.0000	1.0000
F81G	39	-1544.2776	3166.5551	0.0000	1.0000
F81I	39	-1544.4728	3166.9456	0.0000	1.0000
F81IG	40	-1544.2293	3168.4585	0.0000	1.0000
F81	38	-1557.4667	3190.9334	0.0000	1.0000
JC69I	36	-1563.1148	3198.2296	0.0000	1.0000
JC69G	36	-1563.2840	3198.5680	0.0000	1.0000
JC69IG	37	-1563.0313	3200.0627	0.0000	1.0000
JC69	35	-1577.5927	3225.1854	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYG	40	-1499.8277	3243.6682	0.6327	0.6327
HKYI	40	-1500.4808	3244.9745	0.3293	0.9620
HKYIG	41	-1499.8262	3249.7655	0.0300	0.9920
GTRG	44	-1492.2560	3252.9261	0.0062	0.9982
GTRI	44	-1493.6431	3255.7003	0.0015	0.9997
GTRIG	45	-1492.2495	3259.0133	0.0003	1.0000
HKY	39	-1514.3373	3266.5870	0.0000	1.0000
K2PG	37	-1522.0802	3269.8721	0.0000	1.0000
K2PI	37	-1522.2472	3270.2061	0.0000	1.0000
K2PIG	38	-1522.0072	3275.8265	0.0000	1.0000
GTR	43	-1507.7068	3277.7273	0.0000	1.0000
SYMG	41	-1520.7719	3291.6568	0.0000	1.0000
SYMI	41	-1521.2577	3292.6285	0.0000	1.0000
K2P	36	-1536.6618	3292.9350	0.0000	1.0000
SYMIG	42	-1520.6817	3297.5767	0.0000	1.0000
SYM	40	-1536.8572	3317.7272	0.0000	1.0000
F81G	39	-1544.2776	3326.4676	0.0000	1.0000
F81I	39	-1544.4728	3326.8580	0.0000	1.0000
F81IG	40	-1544.2293	3332.4713	0.0000	1.0000
JC69I	36	-1563.1148	3345.8411	0.0000	1.0000
JC69G	36	-1563.2840	3346.1794	0.0000	1.0000
F81	38	-1557.4667	3346.7455	0.0000	1.0000
JC69IG	37	-1563.0313	3351.7745	0.0000	1.0000
JC69	35	-1577.5927	3368.6965	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/chr9_7138.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7138.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/chr9_7138.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7138.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/chr9_7138.phylip = 1 - 446;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr9_7138.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

