Directory src/dr/evomodelxml/substmodel/

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baele.guy@gmail.com 2013-04-10 01:46 Rev.: 5571

Allow the BEAST parser to use the LG amino acid model.

2 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: EmpiricalAminoAcidModelParser.java (+2)

msuchard 2012-11-28 10:34 Rev.: 5260

Incomplete implementation of multi-state stochastic Dollo under BEAGLE. Needs considerably more work.

26 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: MutationDeathModelParser.java (new)

msuchard 2012-02-04 04:38 Rev.: 4638

Bug fix in randomization for SVSComplexSubstitutionModel

6 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: ComplexSubstitutionModelParser.java (new)

rambaut 2011-11-15 05:14 Rev.: 4423

Added citations to amino acid models and a text box in BEAUti.

2 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: EmpiricalAminoAcidModelParser.java (+2)

dong.w.xie 2011-07-07 17:02 Rev.: 4102

GF81

51 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: GeneralF81ModelParser.java (new 51)

msuchard 2011-04-15 08:03 Rev.: 3933

Fixing indicator randomization for reversible models

9 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: GeneralSubstitutionModelParser.java (+9 -1)

akaruiws 2011-04-04 10:17 Rev.: 3925

Correct tag name.

2 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: MsatBMAParser.java (new)

akaruiws 2011-04-01 01:16 Rev.: 3911

Tidy up MsatBMA related things.

302 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: MsatAveragingSubsetModelParser.java (del), MsatBMAParser.java (+302)

dong.w.xie 2011-03-02 09:56 Rev.: 3843

Trunk: solve Issue 438: BEAST should tell you what frequencies belong to which partition

1 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: FrequencyModelParser.java (new)

akaruiws 2011-02-17 15:37 Rev.: 3806

BMA for nucleotide substition models and gamma site model.

2 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: NtdBMAParser.java (new)

akaruiws 2011-02-15 13:00 Rev.: 3798

Model averaging for nucleotide models.

73 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: NtdBMAParser.java (+73)

rambaut 2011-01-24 23:18 Rev.: 3777

Some new empirical codon models by Stefan Zoller (ETH Zurich) & Adrian Schneider (U. of Edinburgh). Example files in examples/release/EmpiricalCodonModels

318 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: EmpiricalCodonModelParser.java (new 164), PCACodonModelParser.java (new 154)

msuchard 2010-09-28 06:44 Rev.: 3582

Fixed GeneralSubstitutionModelParser when relativeTo is not provided.

1 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: GeneralSubstitutionModelParser.java (+1 -1)

akaruiws 2010-09-25 18:02 Rev.: 3572

updates for watkins msat model classes.

54 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: NewMicrosatelliteModelParser.java (new 54)

alexander.alekseyenko 2010-09-24 04:20 Rev.: 3567

fix and move a few example files of my making

6 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: GeneralSubstitutionModelParser.java (+6 -3)

rambaut 2010-07-28 05:46 Rev.: 3327

Forgot a couple of other things...

1 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: ComplexSubstitutionModelParser.java (+1 -1)

rambaut 2010-07-28 05:02 Rev.: 3325

Cleaned up the GeneralSubstitutionModel parser even more. This involved getting rid of SVSIrreversibleSubstModel (old code, Marc promises me). RootFreqs are gone - only worked with the old Irreversible model. Can be done other ways now. svsComplexSubstitutionModel and svsGeneralSubstitutionModel are synonyms of this parser and should allow backwards compatibility.

7 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: GeneralSubstitutionModelParser.java (+7 -22)

rambaut 2010-07-23 03:01 Rev.: 3321

Cleaned up GeneralSubstitutionModelParser so it generally uses SVSGeneralSubstitutionModel or SVSIrreversibleSubstitutionModel (creating indicators = 1 if not specified). The only case now where it will use GeneralSubstitutionModel is if relativeTo attribute is specified.

59 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: GeneralSubstitutionModelParser.java (+59 -42)

dong.w.xie 2010-06-25 10:23 Rev.: 3285

TRUNK: solve Issue 324: "rates" in "svsGeneralSubstitutionModel" should not have relativeTo

5 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: GeneralSubstitutionModelParser.java (+5)

dong.w.xie 2010-06-14 12:47 Rev.: 3263

TRUNK: solve Issue 315: make alias "svsGeneralSubstitutionModel" of "generalSubstitutionModel", Issue 316: previous XML with "generalSubstitutionModel" is not working, and Issue 317: BEAUti: geo-phylogenetic symmetric + no BSSVS xml not working.

10 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: GeneralSubstitutionModelParser.java (+10 -3)

akaruiws 2010-06-11 12:47 Rev.: 3248

Msat model averaging.

252 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: MsatAveragingSubsetModelParser.java (new 252)

rambaut 2010-06-01 20:52 Rev.: 3206

Copied the new all-encompassing GeneralSubstitutionModelParser into dr.app.beagle.parsers to keep BEAST/BEAGLE XML compatibility.

1 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: GeneralSubstitutionModelParser.java (+1 -2)

dong.w.xie 2010-04-13 18:04 Rev.: 3117

TRUNK: sovle Issue 300: have a single parser 'generalSubstitutionModel' and get rid of 'svsGeneralSubstitutionModel' paser

104 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: ComplexSubstitutionModelParser.java (+3 -2), GeneralSubstitutionModelParser.java (+101 -35)

dong.w.xie 2010-03-11 15:05 Rev.: 3036

Trunk: solve Issue 285: ComplexSubstitutionModelParser can only refer to SVS not ComplexSubstitutionModel.

1 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: ComplexSubstitutionModelParser.java (+1 -1)

dong.w.xie 2010-03-03 10:42 Rev.: 3013

Trunk refactoring: finish MULTIVARIATE OU PROCESS (split parsers).

159 lines of code changed in 2 files:

• src/dr/evomodelxml/substmodel: MultivariateOUModelParser.java (new 114), PositiveDefiniteSubstitutionModelParser.java (new 45)

dong.w.xie 2010-03-03 08:46 Rev.: 3012

Trunk refactoring: finish MSSD (split parsers).

83 lines of code changed in 1 file:

• src/dr/evomodelxml/substmodel: MutationDeathModelParser.java (+83)

dong.w.xie 2010-02-17 16:12 Rev.: 2936

Trunk refactoring: make evoxml parsers more organized.

3 lines of code changed in 4 files:

• src/dr/evomodelxml/substmodel: ComplexSubstitutionModelParser.java (+1 -1), FrequencyModelParser.java (+1 -1), GLMSubstitutionModelParser.java (new)

dong.w.xie 2010-02-17 16:04 Rev.: 2935

Trunk refactoring: make subst parsers more organized.

1874 lines of code changed in 20 files:

• src/dr/evomodelxml/substmodel: AsymQuadModelParser.java (new 105), BinaryCovarionModelParser.java (new 82), BinarySubstitutionModelParser.java (new 60), ComplexSubstitutionModelParser.java (+155), CovarionGTRParser.java (new 103), CovarionHKYParser.java (new 79), EmpiricalAminoAcidModelParser.java (+73), FrequencyModelParser.java (+124), GLMSubstitutionModelParser.java (+75), GTRParser.java (new 122), GeneralSubstitutionModelParser.java (+103), HKYParser.java (new 58), LewisMkSubstitutionModelParser.java (new 151), LinearBiasModelParser.java (new 104), MkModelParser.java (new 85), SubstitutionEpochModelParser.java (new 74), TN93Parser.java (new 65), TwoPhaseModelParser.java (new 77), TwoStateCovarionModelParser.java (new 77), YangCodonModelParser.java (new 102)