
Output from mraic.pl version 1.4.4 by Johan Nylander
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12:12 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/chr4_10530.phylip" (19 taxa, 256 characters)

Minimum AIC  model: SYMG
Minimum AICc model: SYMG
Minimum BIC  model: K2P


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
SYMG	41	-592.8799	1283.8532	0.2702	0.2702
SYMI	41	-593.0906	1284.2746	0.2189	0.4890
SYM	40	-594.9607	1285.1773	0.1394	0.6284
K2PG	37	-599.6332	1286.1656	0.0850	0.7134
K2PI	37	-599.7461	1286.3914	0.0759	0.7894
SYMIG	42	-592.8595	1286.6768	0.0658	0.8552
K2P	36	-601.5593	1287.2829	0.0486	0.9038
K2PIG	38	-599.6244	1288.9077	0.0216	0.9254
JC69G	36	-602.5985	1289.3613	0.0172	0.9426
JC69I	36	-602.7130	1289.5903	0.0153	0.9580
JC69	35	-604.4328	1290.3202	0.0107	0.9686
GTRG	44	-592.1285	1291.0247	0.0075	0.9761
GTRI	44	-592.3446	1291.4569	0.0060	0.9821
JC69IG	37	-602.5909	1292.0809	0.0044	0.9866
GTR	43	-594.1928	1292.2347	0.0041	0.9906
HKYG	40	-599.0831	1293.4220	0.0023	0.9929
HKYI	40	-599.1924	1293.6407	0.0020	0.9949
GTRIG	45	-592.1088	1293.9320	0.0018	0.9967
HKY	39	-601.0127	1294.4698	0.0013	0.9980
HKYIG	41	-599.0745	1296.2424	0.0006	0.9986
F81G	39	-601.9710	1296.3864	0.0005	0.9991
F81I	39	-602.0840	1296.6125	0.0005	0.9995
F81	38	-603.8025	1297.2639	0.0003	0.9999
F81IG	40	-601.9638	1299.1835	0.0001	1.0000



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

Model	df	lnL		AIC		wAIC	cwAIC
SYMG	41	-592.8799	1267.7597	0.3331	0.3331
SYMI	41	-593.0906	1268.1812	0.2698	0.6030
SYMIG	42	-592.8595	1269.7190	0.1251	0.7280
SYM	40	-594.9607	1269.9214	0.1130	0.8411
GTRG	44	-592.1285	1272.2569	0.0352	0.8762
GTRI	44	-592.3446	1272.6891	0.0283	0.9046
K2PG	37	-599.6332	1273.2665	0.0212	0.9258
K2PI	37	-599.7461	1273.4923	0.0190	0.9447
GTRIG	45	-592.1088	1274.2177	0.0132	0.9579
GTR	43	-594.1928	1274.3856	0.0121	0.9701
K2P	36	-601.5593	1275.1186	0.0084	0.9785
K2PIG	38	-599.6244	1275.2487	0.0079	0.9864
JC69G	36	-602.5985	1277.1970	0.0030	0.9893
JC69I	36	-602.7130	1277.4259	0.0027	0.9920
HKYG	40	-599.0831	1278.1662	0.0018	0.9938
HKYI	40	-599.1924	1278.3849	0.0016	0.9955
JC69	35	-604.4328	1278.8656	0.0013	0.9967
JC69IG	37	-602.5909	1279.1818	0.0011	0.9978
HKY	39	-601.0127	1280.0254	0.0007	0.9986
HKYIG	41	-599.0745	1280.1489	0.0007	0.9993
F81G	39	-601.9710	1281.9420	0.0003	0.9995
F81I	39	-602.0840	1282.1680	0.0002	0.9998
F81	38	-603.8025	1283.6049	0.0001	0.9999
F81IG	40	-601.9638	1283.9277	0.0001	1.0000



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

Model	df	lnL		BIC		wBIC	cwBIC
K2P	36	-601.5593	1402.7449	0.2892	0.2892
JC69	35	-604.4328	1402.9469	0.2614	0.5506
K2PG	37	-599.6332	1404.4380	0.1240	0.6747
K2PI	37	-599.7461	1404.6638	0.1108	0.7855
JC69G	36	-602.5985	1404.8233	0.1023	0.8878
JC69I	36	-602.7130	1405.0523	0.0912	0.9790
K2PIG	38	-599.6244	1409.9654	0.0078	0.9868
JC69IG	37	-602.5909	1410.3534	0.0064	0.9933
SYM	40	-594.9607	1411.7285	0.0032	0.9965
SYMG	41	-592.8799	1413.1120	0.0016	0.9981
SYMI	41	-593.0906	1413.5334	0.0013	0.9995
HKY	39	-601.0127	1418.2873	0.0001	0.9996
F81	38	-603.8025	1418.3217	0.0001	0.9997
SYMIG	42	-592.8595	1418.6165	0.0001	0.9998
HKYG	40	-599.0831	1419.9733	0.0001	0.9999
HKYI	40	-599.1924	1420.1920	0.0000	0.9999
F81G	39	-601.9710	1420.2039	0.0000	0.9999
F81I	39	-602.0840	1420.4300	0.0000	1.0000
HKYIG	41	-599.0745	1425.5012	0.0000	1.0000
F81IG	40	-601.9638	1425.7348	0.0000	1.0000
GTR	43	-594.1928	1426.8282	0.0000	1.0000
GTRG	44	-592.1285	1428.2447	0.0000	1.0000
GTRI	44	-592.3446	1428.6769	0.0000	1.0000
GTRIG	45	-592.1088	1433.7507	0.0000	1.0000



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

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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10530.phylip = 1 - 256;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10530.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=Fixed(Equal);
END;


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

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10530.phylip = 1 - 256;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10530.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=Fixed(Equal);
END;


[Mrbayes block for the best BIC model (K2P)]

BEGIN MRBAYES;
 Charset /Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10530.phylip = 1 - 256;
 Partition Dummy = 1:/Users/bcf/Git/brant/seqcap/Manuscripts/Tetrapods/Nature/Data/917Loci_19Species/alignments_from_loci/917Loci_19Species_alignments_phylip/chr4_10530.phylip;
 Set partition = Dummy;
 Lset applyto=(1) nst=2 rates=equal;
 Prset applyto=(1) statefreqpr=Fixed(Equal) tratiopr=Beta(1.0,1.0);
END;


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End of Output

