
Output from mraic.pl version 1.4.4 by Johan Nylander
-------------------------------------------------------------
11:03 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/chr11_3432.phylip" (19 taxa, 234 characters)

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


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	-536.3382	1169.6711	0.3674	0.3674
HKYG	40	-536.4613	1169.9174	0.3248	0.6922
HKY	39	-538.7956	1171.6738	0.1350	0.8271
HKYIG	41	-536.4623	1172.8622	0.0745	0.9016
GTRI	44	-532.7908	1174.5339	0.0323	0.9339
GTRG	44	-532.8612	1174.6749	0.0301	0.9640
GTR	43	-534.9907	1175.8973	0.0163	0.9804
GTRIG	45	-532.8652	1177.7518	0.0065	0.9868
F81I	39	-541.9519	1177.9863	0.0057	0.9926
F81G	39	-542.1174	1178.3173	0.0049	0.9975
F81	38	-544.8023	1180.8046	0.0014	0.9989
F81IG	40	-542.1127	1181.2202	0.0011	1.0000
K2PI	37	-553.8011	1195.9491	0.0000	1.0000
K2PG	37	-553.9615	1196.2700	0.0000	1.0000
K2P	36	-556.7669	1199.0566	0.0000	1.0000
K2PIG	38	-553.9625	1199.1250	0.0000	1.0000
SYMI	41	-552.0654	1204.0684	0.0000	1.0000
SYMG	41	-552.2198	1204.3772	0.0000	1.0000
JC69I	36	-559.6827	1204.8882	0.0000	1.0000
JC69G	36	-559.8645	1205.2518	0.0000	1.0000
SYM	40	-554.3196	1205.6341	0.0000	1.0000
SYMIG	42	-552.2196	1207.3502	0.0000	1.0000
JC69	35	-562.6179	1207.9630	0.0000	1.0000
JC69IG	37	-559.8597	1208.0664	0.0000	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
HKYI	40	-536.3382	1152.6763	0.2438	0.2438
HKYG	40	-536.4613	1152.9226	0.2155	0.4593
GTRI	44	-532.7908	1153.5815	0.1550	0.6143
GTRG	44	-532.8612	1153.7225	0.1445	0.7588
HKYIG	41	-536.4623	1154.9247	0.0792	0.8380
HKY	39	-538.7956	1155.5913	0.0568	0.8948
GTRIG	45	-532.8652	1155.7305	0.0529	0.9477
GTR	43	-534.9907	1155.9815	0.0467	0.9944
F81I	39	-541.9519	1161.9038	0.0024	0.9968
F81G	39	-542.1174	1162.2348	0.0020	0.9989
F81IG	40	-542.1127	1164.2254	0.0008	0.9996
F81	38	-544.8023	1165.6046	0.0004	1.0000
K2PI	37	-553.8011	1181.6022	0.0000	1.0000
K2PG	37	-553.9615	1181.9231	0.0000	1.0000
K2PIG	38	-553.9625	1183.9250	0.0000	1.0000
K2P	36	-556.7669	1185.5338	0.0000	1.0000
SYMI	41	-552.0654	1186.1309	0.0000	1.0000
SYMG	41	-552.2198	1186.4397	0.0000	1.0000
SYMIG	42	-552.2196	1188.4392	0.0000	1.0000
SYM	40	-554.3196	1188.6393	0.0000	1.0000
JC69I	36	-559.6827	1191.3653	0.0000	1.0000
JC69G	36	-559.8645	1191.7290	0.0000	1.0000
JC69IG	37	-559.8597	1193.7195	0.0000	1.0000
JC69	35	-562.6179	1195.2357	0.0000	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
HKY	39	-538.7956	1290.3488	0.3842	0.3842
HKYI	40	-536.3382	1290.8891	0.2932	0.6774
HKYG	40	-536.4613	1291.1355	0.2593	0.9367
HKYIG	41	-536.4623	1296.5928	0.0169	0.9536
F81I	39	-541.9519	1296.6613	0.0164	0.9700
F81	38	-544.8023	1296.9068	0.0145	0.9845
F81G	39	-542.1174	1296.9923	0.0139	0.9983
F81IG	40	-542.1127	1302.4382	0.0009	0.9992
GTR	43	-534.9907	1304.5603	0.0003	0.9996
GTRI	44	-532.7908	1305.6156	0.0002	0.9997
GTRG	44	-532.8612	1305.7566	0.0002	0.9999
K2PI	37	-553.8011	1309.4491	0.0000	0.9999
K2PG	37	-553.9615	1309.7700	0.0000	1.0000
K2P	36	-556.7669	1309.9253	0.0000	1.0000
GTRIG	45	-532.8652	1311.2200	0.0000	1.0000
K2PIG	38	-553.9625	1315.2272	0.0000	1.0000
JC69I	36	-559.6827	1315.7569	0.0000	1.0000
JC69G	36	-559.8645	1316.1206	0.0000	1.0000
JC69	35	-562.6179	1316.1720	0.0000	1.0000
JC69IG	37	-559.8597	1321.5664	0.0000	1.0000
SYM	40	-554.3196	1326.8521	0.0000	1.0000
SYMI	41	-552.0654	1327.7990	0.0000	1.0000
SYMG	41	-552.2198	1328.1079	0.0000	1.0000
SYMIG	42	-552.2196	1333.5626	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/chr11_3432.phylip = 1 - 234;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3432.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/chr11_3432.phylip = 1 - 234;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3432.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 (HKY)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3432.phylip = 1 - 234;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr11_3432.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Dirichlet(1.0,1.0,1.0,1.0) tratiopr=Beta(1.0,1.0);
END;


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End of Output

