
Output from mraic.pl version 1.4.4 by Johan Nylander
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11:26 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_3015.phylip" (19 taxa, 341 characters)

Minimum AIC  model: HKYI
Minimum AICc model: HKYI
Minimum BIC  model: HKYI


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
HKYI	40	-961.0548	2013.0429	0.5166	0.5166
HKYG	40	-961.7419	2014.4171	0.2599	0.7765
HKYIG	41	-961.0740	2015.6665	0.1391	0.9156
GTRI	44	-958.3453	2018.0690	0.0419	0.9574
GTRG	44	-958.9298	2019.2380	0.0233	0.9808
GTRIG	45	-958.3610	2020.7559	0.0109	0.9917
HKY	39	-966.6681	2021.7017	0.0068	0.9985
GTR	43	-963.8716	2026.4840	0.0006	0.9991
K2PI	37	-972.1186	2027.5177	0.0004	0.9995
K2PG	37	-972.1360	2027.5526	0.0004	0.9999
K2PIG	38	-972.1374	2030.0893	0.0001	1.0000
SYMI	41	-970.1568	2033.8320	0.0000	1.0000
SYMG	41	-970.6023	2034.7229	0.0000	1.0000
K2P	36	-977.4147	2035.5925	0.0000	1.0000
SYMIG	42	-970.1717	2036.4643	0.0000	1.0000
SYM	40	-974.9935	2040.9203	0.0000	1.0000
F81I	39	-990.8768	2070.1191	0.0000	1.0000
F81G	39	-991.3388	2071.0431	0.0000	1.0000
F81IG	40	-990.8895	2072.7123	0.0000	1.0000
F81	38	-995.9195	2077.6536	0.0000	1.0000
JC69I	36	-999.7719	2080.3070	0.0000	1.0000
JC69G	36	-1000.2335	2081.2302	0.0000	1.0000
JC69IG	37	-999.7845	2082.8495	0.0000	1.0000
JC69	35	-1004.4419	2087.1461	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-961.0548	2002.1095	0.4157	0.4157
HKYG	40	-961.7419	2003.4837	0.2091	0.6248
HKYIG	41	-961.0740	2004.1481	0.1500	0.7748
GTRI	44	-958.3453	2004.6906	0.1144	0.8891
GTRG	44	-958.9298	2005.8596	0.0637	0.9529
GTRIG	45	-958.3610	2006.7220	0.0414	0.9943
HKY	39	-966.6681	2011.3363	0.0041	0.9984
GTR	43	-963.8716	2013.7433	0.0012	0.9997
K2PI	37	-972.1186	2018.2371	0.0001	0.9998
K2PG	37	-972.1360	2018.2721	0.0001	0.9999
K2PIG	38	-972.1374	2020.2747	0.0000	1.0000
SYMI	41	-970.1568	2022.3136	0.0000	1.0000
SYMG	41	-970.6023	2023.2045	0.0000	1.0000
SYMIG	42	-970.1717	2024.3435	0.0000	1.0000
K2P	36	-977.4147	2026.8294	0.0000	1.0000
SYM	40	-974.9935	2029.9869	0.0000	1.0000
F81I	39	-990.8768	2059.7537	0.0000	1.0000
F81G	39	-991.3388	2060.6777	0.0000	1.0000
F81IG	40	-990.8895	2061.7789	0.0000	1.0000
F81	38	-995.9195	2067.8390	0.0000	1.0000
JC69I	36	-999.7719	2071.5438	0.0000	1.0000
JC69G	36	-1000.2335	2072.4671	0.0000	1.0000
JC69IG	37	-999.7845	2073.5689	0.0000	1.0000
JC69	35	-1004.4419	2078.8838	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKYI	40	-961.0548	2155.3848	0.5453	0.5453
HKYG	40	-961.7419	2156.7590	0.2743	0.8196
K2PI	37	-972.1186	2160.0168	0.0538	0.8735
K2PG	37	-972.1360	2160.0518	0.0529	0.9263
HKY	39	-966.6681	2160.7797	0.0367	0.9631
HKYIG	41	-961.0740	2161.2553	0.0290	0.9920
K2P	36	-977.4147	2164.7771	0.0050	0.9970
K2PIG	38	-972.1374	2165.8863	0.0029	0.9999
GTRI	44	-958.3453	2173.2934	0.0001	0.9999
GTRG	44	-958.9298	2174.4624	0.0000	1.0000
GTR	43	-963.8716	2178.5142	0.0000	1.0000
GTRIG	45	-958.3610	2179.1567	0.0000	1.0000
SYMI	41	-970.1568	2179.4208	0.0000	1.0000
SYMG	41	-970.6023	2180.3117	0.0000	1.0000
SYM	40	-974.9935	2183.2622	0.0000	1.0000
SYMIG	42	-970.1717	2185.2826	0.0000	1.0000
F81I	39	-990.8768	2209.1971	0.0000	1.0000
JC69I	36	-999.7719	2209.4916	0.0000	1.0000
F81G	39	-991.3388	2210.1211	0.0000	1.0000
JC69G	36	-1000.2335	2210.4148	0.0000	1.0000
JC69	35	-1004.4419	2212.9997	0.0000	1.0000
F81	38	-995.9195	2213.4505	0.0000	1.0000
F81IG	40	-990.8895	2215.0542	0.0000	1.0000
JC69IG	37	-999.7845	2215.3486	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3015.phylip = 1 - 341;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3015.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3015.phylip = 1 - 341;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3015.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3015.phylip = 1 - 341;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr17_3015.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=propinv;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0) pinvarpr=Uniform(0.0,1.0);
END;


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End of Output

