[root]
bin
(0 files, 0 lines)
doc
(8 files, 112 lines)
BookSection
(12 files, 6 lines)
EBSP
(1 files, 0 lines)
mystery-mammal
(0 files, 0 lines)
mystery-run-1
(5 files, 0 lines)
scripts
(0 files, 0 lines)
PackageStructure
(4 files, 125 lines)
StarBEAST
(1 files, 0 lines)
figures
(20 files, 0 lines)
Virus Practical Tex
(0 files, 0 lines)
figures1
(14 files, 0 lines)
figures2
(7 files, 0 lines)
figures3
(4 files, 0 lines)
tutorial
(0 files, 0 lines)
BSP
(7 files, 6877 lines)
figures3
(10 files, 0 lines)
DivergenceDating
(1 files, 24 lines)
1.1a_Primates
(2 files, 423 lines)
latex
(1 files, 585 lines)
figures
(19 files, 0 lines)
1.2_Primates
(4 files, 3 lines)
latex
(2 files, -2 lines)
figures
(19 files, -825 lines)
EBSP
(0 files, 0 lines)
flu
(2 files, 512 lines)
figures
(14 files, 814 lines)
StarBEAST
(3 files, 1477 lines)
figures
(11 files, 0 lines)
Virus Practical Tex
(0 files, 0 lines)
figures3
(0 files, 0 lines)
Virus_Practical_1_6_1
(2 files, 1007 lines)
figures1
(17 files, 0 lines)
figures2
(9 files, 0 lines)
figures3
(9 files, 0 lines)
examples
(1 files, 5 lines)
Data
(0 files, 0 lines)
Phylogeography
(0 files, 0 lines)
continuous
(0 files, 0 lines)
beauti1.5
(0 files, 0 lines)
Gopher data
(0 files, 0 lines)
Virus Practical
(0 files, 0 lines)
FPV
(0 files, 0 lines)
Flu
(0 files, 0 lines)
RSVA
(0 files, 0 lines)
starBEAST
(0 files, 0 lines)
treePrior+clockModel
(0 files, 0 lines)
beauti1.6
(0 files, 0 lines)
codon
(0 files, 0 lines)
starBEAST
(0 files, 0 lines)
treePrior+clockModel
(0 files, 0 lines)
calibrations
(0 files, 0 lines)
incorrect
(19 files, 6019 lines)
treePriors
(2 files, 422 lines)
moa
(0 files, 0 lines)
mountainLion
(0 files, 0 lines)
release
(0 files, 0 lines)
Benchmarks
(3 files, 362 lines)
Data
(2 files, 51 lines)
EmpiricalCodonModels
(2 files, 421 lines)
codon-data
(0 files, 0 lines)
ecmdata
(6 files, 6 lines)
pcadata
(5 files, 104 lines)
Phylogeography
(0 files, 0 lines)
continuous
(3 files, 2252 lines)
calibrations
(17 files, 1234 lines)
clockModels
(9 files, 2329 lines)
continuousTraits
(2 files, 41 lines)
discreteTraits
(2 files, 209 lines)
microsatellite
(1 files, 1012 lines)
recombination
(3 files, 10494 lines)
starBEAST
(0 files, 0 lines)
substModels
(0 files, 0 lines)
testXML
(35 files, 10012 lines)
treePrior+clockModel
(8 files, 2540 lines)
treePrior+clockModel
(0 files, 0 lines)
treePriors
(0 files, 0 lines)
treeOpsTest
(0 files, 0 lines)
treePriors
(0 files, 0 lines)
unrelease
(7 files, 2405 lines)
icons
(0 files, 0 lines)
lib
(14 files, 0 lines)
native
(12 files, 4027 lines)
deprecated
(5 files, 933 lines)
expokit
(0 files, 0 lines)
plugins_SDK
(2 files, 188 lines)
templates
(6 files, 550 lines)
release
(0 files, 0 lines)
Launch4j
(0 files, 0 lines)
bin
(0 files, 0 lines)
head
(0 files, 0 lines)
lib
(0 files, 0 lines)
manifest
(0 files, 0 lines)
w32api
(0 files, 0 lines)
Linux
(0 files, 0 lines)
lib
(2 files, 0 lines)
scripts
(7 files, 53 lines)
Mac
(0 files, 0 lines)
lib
(6 files, 0 lines)
scripts
(7 files, 54 lines)
Windows
(7 files, 0 lines)
lib
(2 files, 0 lines)
scripts
(7 files, 35 lines)
common
(2 files, 4 lines)
doc
(5 files, 21003 lines)
examples
(0 files, 0 lines)
Data
(0 files, 0 lines)
Gopher Data
(0 files, 0 lines)
Phylogeography
(0 files, 0 lines)
Virus Practical
(0 files, 0 lines)
FPV
(0 files, 0 lines)
Flu
(0 files, 0 lines)
RSVA
(0 files, 0 lines)
beauti1.5
(0 files, 0 lines)
Gopher Data
(0 files, 0 lines)
Virus Practical
(0 files, 0 lines)
FPV
(0 files, 0 lines)
Flu
(0 files, 0 lines)
RSVA
(0 files, 0 lines)
starBEAST
(0 files, 0 lines)
treePrior+clockModel
(0 files, 0 lines)
calibrations
(0 files, 0 lines)
starBEAST
(0 files, 0 lines)
treePrior+clockModel
(0 files, 0 lines)
treePriors
(0 files, 0 lines)
icons
(14 files, 0 lines)
native
(0 files, 0 lines)
extra_lib
(0 files, 0 lines)
release_phylogeography
(0 files, 0 lines)
common
(1 files, 8 lines)
bin
(5 files, 135 lines)
lib
(1 files, 0 lines)
src
(0 files, 0 lines)
dr
(1 files, -5 lines)
app
(0 files, 0 lines)
SnAPhyl
(0 files, 0 lines)
datapanel
(0 files, 0 lines)
images
(4 files, 0 lines)
initializationpanel
(0 files, 0 lines)
mcmcpanel
(0 files, 0 lines)
operatorspanel
(0 files, 0 lines)
priorsPanel
(0 files, 0 lines)
util
(0 files, 0 lines)
beagle
(0 files, 0 lines)
evomodel
(0 files, 0 lines)
branchmodel
(5 files, 31 lines)
branchratemodel
(0 files, 0 lines)
operators
(1 files, -6 lines)
parsers
(38 files, 850 lines)
sitemodel
(6 files, 0 lines)
substmodel
(35 files, 609 lines)
treelikelihood
(14 files, 1342 lines)
utilities
(4 files, 47 lines)
tools
(3 files, -640 lines)
parsers
(3 files, 25 lines)
beast
(12 files, 719 lines)
beastdev
(0 files, 0 lines)
beauti
(7 files, 645 lines)
alignmentviewer
(17 files, 1061 lines)
ancestralStatesPanel
(2 files, 8 lines)
clockModelsPanel
(3 files, 2 lines)
components
(1 files, 13 lines)
ancestralstates
(3 files, 79 lines)
continuous
(4 files, 54 lines)
discrete
(4 files, 38 lines)
dnds
(0 files, 0 lines)
dollo
(3 files, 68 lines)
hpm
(4 files, 38 lines)
sequenceerror
(3 files, 36 lines)
tipdatesampling
(3 files, 63 lines)
datapanel
(7 files, 110 lines)
enumTypes
(0 files, 0 lines)
generator
(17 files, 92 lines)
mcmcpanel
(1 files, 0 lines)
modelsPanel
(0 files, 0 lines)
operatorspanel
(1 files, 0 lines)
options
(25 files, 133 lines)
priorsPanel
(8 files, 52 lines)
siteModelsPanel
(3 files, -2 lines)
taxonsetspanel
(2 files, 25 lines)
tipdatepanel
(4 files, 125 lines)
traitspanel
(5 files, 55 lines)
treespanel
(7 files, 1 lines)
types
(19 files, 409 lines)
util
(11 files, 168 lines)
bfe
(8 files, 744 lines)
bss
(34 files, 619 lines)
icons
(8 files, 0 lines)
test
(1 files, -5 lines)
coalgen
(8 files, 6 lines)
images
(5 files, 0 lines)
gui
(4 files, 61 lines)
chart
(27 files, 1462 lines)
components
(4 files, 11 lines)
table
(8 files, 796 lines)
images
(2 files, 0 lines)
tree
(7 files, 1236 lines)
util
(5 files, 376 lines)
java16compat
(0 files, 0 lines)
mapper
(0 files, 0 lines)
application
(8 files, 2348 lines)
images
(2 files, 0 lines)
mapper
(5 files, 139 lines)
menus
(4 files, 273 lines)
misc
(1 files, 405 lines)
oldbeauti
(22 files, 1363 lines)
images
(4 files, 0 lines)
pathogen
(12 files, 461 lines)
images
(5 files, 0 lines)
phylogeography
(0 files, 0 lines)
builder
(0 files, 0 lines)
generator
(0 files, 0 lines)
gui
(0 files, 0 lines)
spread
(0 files, 0 lines)
images
(0 files, 0 lines)
inputpanel
(0 files, 0 lines)
layerspanel
(0 files, 0 lines)
renderpanel
(0 files, 0 lines)
structure
(0 files, 0 lines)
tools
(8 files, 993 lines)
kml
(9 files, 527 lines)
plugin
(2 files, 1 lines)
seqgen
(5 files, 32 lines)
tools
(27 files, 2802 lines)
tracer
(0 files, 0 lines)
analysis
(13 files, 12 lines)
application
(10 files, 61 lines)
images
(2 files, 0 lines)
images
(2 files, 0 lines)
traces
(18 files, 192 lines)
images
(5 files, 0 lines)
treespace
(12 files, 651 lines)
inputpanel
(2 files, 389 lines)
renderpanel
(1 files, 16 lines)
treestat
(7 files, 2196 lines)
statistics
(21 files, 1897 lines)
util
(3 files, 712 lines)
vcs
(3 files, 3 lines)
evolution
(3 files, 121 lines)
alignment
(15 files, 3765 lines)
coalescent
(27 files, 4279 lines)
structure
(5 files, 770 lines)
colouring
(11 files, 3239 lines)
continuous
(1 files, 359 lines)
datatype
(19 files, 2368 lines)
distance
(4 files, 523 lines)
geo
(0 files, 0 lines)
io
(9 files, 2582 lines)
parsimony
(1 files, 317 lines)
sequence
(2 files, 503 lines)
tree
(30 files, 4689 lines)
util
(7 files, 1084 lines)
wrightfisher
(5 files, 1010 lines)
evomodel
(0 files, 0 lines)
MSSD
(6 files, 24 lines)
alternativesplicing
(0 files, 0 lines)
antigenic
(15 files, 1084 lines)
approxPopTree
(5 files, 235 lines)
arg
(21 files, 738 lines)
branchratemodel
(1 files, -6 lines)
coalescent
(3 files, -3 lines)
likelihood
(2 files, 12 lines)
operators
(10 files, -14 lines)
beagle
(0 files, 0 lines)
parsers
(0 files, 0 lines)
sitemodel
(0 files, 0 lines)
substmodel
(0 files, 0 lines)
treelikelihood
(0 files, 0 lines)
branchratemodel
(20 files, 1690 lines)
clock
(4 files, -5 lines)
coalescent
(45 files, 1840 lines)
operators
(7 files, 501 lines)
structure
(4 files, 1009 lines)
continuous
(33 files, 1520 lines)
plink
(1 files, 67 lines)
epidemiology
(13 files, 1439 lines)
casetocase
(12 files, 117 lines)
ibd
(3 files, 44 lines)
indel
(7 files, 2301 lines)
newsubstmodel
(0 files, 0 lines)
newtreelikelihood
(11 files, 20 lines)
operators
(49 files, 2430 lines)
randomYule
(0 files, 0 lines)
simulator
(1 files, 193 lines)
sitemodel
(13 files, 2228 lines)
speciation
(39 files, 781 lines)
ModelAveragingResearch
(4 files, 448 lines)
substmodel
(54 files, 6390 lines)
transmission
(6 files, 1491 lines)
tree
(48 files, 5267 lines)
randomlocalmodel
(4 files, 42 lines)
treelikelihood
(26 files, 4834 lines)
evomodelxml
(7 files, 413 lines)
MSSD
(6 files, 289 lines)
branchratemodel
(14 files, 501 lines)
clock
(2 files, 149 lines)
coalescent
(35 files, 1879 lines)
operators
(6 files, 371 lines)
indel
(3 files, 164 lines)
operators
(28 files, 1050 lines)
sitemodel
(7 files, 388 lines)
speciation
(35 files, 1088 lines)
substmodel
(29 files, 1965 lines)
tree
(27 files, 962 lines)
treelikelihood
(7 files, 29 lines)
evoxml
(36 files, 2635 lines)
util
(4 files, 400 lines)
exporters
(0 files, 0 lines)
geo
(36 files, 5718 lines)
cartogram
(1 files, 23 lines)
contouring
(8 files, 1612 lines)
distributions
(4 files, 92 lines)
math
(3 files, 467 lines)
operators
(2 files, 219 lines)
gui
(0 files, 0 lines)
chart
(0 files, 0 lines)
graph
(0 files, 0 lines)
table
(0 files, 0 lines)
images
(0 files, 0 lines)
tree
(0 files, 0 lines)
inference
(0 files, 0 lines)
distribution
(31 files, 2427 lines)
loggers
(12 files, 1106 lines)
markovchain
(4 files, 521 lines)
markovjumps
(7 files, 111 lines)
mcmc
(4 files, 584 lines)
mcmcmc
(2 files, 588 lines)
ml
(1 files, 289 lines)
model
(75 files, 4385 lines)
operators
(59 files, 2303 lines)
parallel
(4 files, 85 lines)
prior
(11 files, 828 lines)
trace
(26 files, 2366 lines)
tutorial
(1 files, 0 lines)
xml
(0 files, 0 lines)
inferencexml
(2 files, 70 lines)
distribution
(26 files, 1353 lines)
loggers
(3 files, 101 lines)
model
(32 files, 1527 lines)
operators
(31 files, 1316 lines)
trace
(6 files, 436 lines)
java16compat
(0 files, 0 lines)
math
(21 files, 4075 lines)
distributions
(33 files, 1354 lines)
functionEval
(1 files, 363 lines)
interfaces
(1 files, 39 lines)
matrixAlgebra
(8 files, 3456 lines)
matrix
(3 files, 1169 lines)
stats
(3 files, 581 lines)
util
(26 files, 1919 lines)
xml
(25 files, 3248 lines)
org
(0 files, 0 lines)
virion
(0 files, 0 lines)
jam
(0 files, 0 lines)
framework
(0 files, 0 lines)
mac
(0 files, 0 lines)
table
(0 files, 0 lines)
images
(0 files, 0 lines)
test
(0 files, 0 lines)
dr
(0 files, 0 lines)
app
(0 files, 0 lines)
beagle
(4 files, 70 lines)
beauti
(2 files, 73 lines)
beauti
(0 files, 0 lines)
calibration
(1 files, 0 lines)
distibutions
(6 files, 2 lines)
evolution
(1 files, 101 lines)
evomodel
(0 files, 0 lines)
arg
(0 files, 0 lines)
operators
(1 files, 3 lines)
branchratemodel
(3 files, 2 lines)
coalescent
(1 files, 0 lines)
operators
(9 files, 424 lines)
sitemodel
(1 files, 262 lines)
speciation
(6 files, 36 lines)
substmodel
(23 files, 1038 lines)
treelikelihood
(6 files, -49 lines)
inference
(0 files, 0 lines)
distribution
(1 files, 4 lines)
mcmc
(1 files, 1 lines)
model
(1 files, 32 lines)
operators
(1 files, 0 lines)
prior
(1 files, 4 lines)
trace
(1 files, 49 lines)
integration
(3 files, 155 lines)
math
(6 files, 21 lines)
Author | Changes | Lines of Code | Lines per Change |
---|---|---|---|
Totals | 230 (100.0%) | 6017 (100.0%) | 26.1 |
dong.w.xie | 77 (33.5%) | 2799 (46.5%) | 36.3 |
rambaut | 93 (40.4%) | 1712 (28.5%) | 18.4 |
alexei.drummond | 10 (4.3%) | 515 (8.6%) | 51.5 |
fbielejec | 11 (4.8%) | 462 (7.7%) | 42.0 |
msuchard | 14 (6.1%) | 323 (5.4%) | 23.0 |
benjamin.redelings | 5 (2.2%) | 113 (1.9%) | 22.6 |
dong.w.xie@gmail.com | 1 (0.4%) | 32 (0.5%) | 32.0 |
mdhall272@gmail.com | 2 (0.9%) | 22 (0.4%) | 11.0 |
Sebastian.Hoehna | 1 (0.4%) | 10 (0.2%) | 10.0 |
sidneym | 5 (2.2%) | 8 (0.1%) | 1.6 |
nawi214 | 1 (0.4%) | 6 (0.1%) | 6.0 |
sibon.li | 5 (2.2%) | 5 (0.1%) | 1.0 |
akaruiws | 2 (0.9%) | 5 (0.1%) | 2.5 |
mtholder | 1 (0.4%) | 2 (0.0%) | 2.0 |
jheled | 1 (0.4%) | 2 (0.0%) | 2.0 |
beth.shapiro | 1 (0.4%) | 1 (0.0%) | 1.0 |
updated buildfile
2 lines of code changed in 2 files:
get the save paths right
13 lines of code changed in 1 file:
had to manually repair org.virion.jam imports to fix ant build problem
2 lines of code changed in 1 file:
updated buildfile
5 lines of code changed in 1 file:
updated buildfile
119 lines of code changed in 1 file:
Merging version stuff and copyright dates with 1.7 branch.
8 lines of code changed in 4 files:
adding multiple trees
18 lines of code changed in 2 files:
Ooops. Reverted.
18 lines of code changed in 1 file:
Committed work to date on network reconstruction method
4 lines of code changed in 1 file:
commiting parser changes
125 lines of code changed in 1 file:
Put the target JDK version as a property at the top of the ant file.
3 lines of code changed in 1 file:
ant buildfile for bss
158 lines of code changed in 1 file:
Fixed an issue in BEAUti with robust counting XML generated where completely gapped sites were being stripped (these are sometimes used to maintain reading frame).
2 lines of code changed in 1 file:
Removing 'blue.jar' from lib folder. Need to work out other solution - either it is part of BEAST or it isn't.
1 lines of code changed in 3 files:
Commented out all of my last commit until issues resolved
2 lines of code changed in 2 files:
Added blue-beast.jar and modified build xmls
3 lines of code changed in 3 files:
Tracer ant file fixes
3 lines of code changed in 1 file:
Updated Tracer ant file libs
1 lines of code changed in 1 file:
trunk: merge BEAST MC3 changes
32 lines of code changed in 1 file:
A few final adjustments for 1.7 packaging.
1 lines of code changed in 1 file:
Addition to the Mac section of the ANT build to associate new BEAUti documents with the application.
9 lines of code changed in 1 file:
trunk: tidy up native/ folder but it needs Andrew to update all Makefiles before deleting compile scripts
435 lines of code changed in 1 file:
trunk: move the remaining native folder under the root of project for easy finding.
6 lines of code changed in 3 files:
changed dependency to commons-math-2.2
20 lines of code changed in 1 file:
Updated ANT script to use new commons maths lib.
2 lines of code changed in 1 file:
uncommitting an erroneous revision
0 lines of code changed in 4 files:
Trunk: add target to create beastTest.jar and change build into jdk 1.6 for BEAST 1.7.
11 lines of code changed in 1 file:
Pathogen updates
1 lines of code changed in 1 file:
Minor modification
2 lines of code changed in 1 file:
Minor modification
2 lines of code changed in 1 file:
Added package building to the phylogeography ant file.
31 lines of code changed in 1 file:
Created an ANT file for phylogeography stuff.
76 lines of code changed in 1 file:
Final tweaks to new version of Pathogen
9 lines of code changed in 1 file:
updating version number in build.xml
2 lines of code changed in 1 file:
Trunk: more JUnit tests
2 lines of code changed in 1 file:
Trunk: merge issue 399 from branch 1.6
1 lines of code changed in 1 file:
Trunk: fix build bug maing release failed
6 lines of code changed in 3 files:
Trunk: solve Issue 389: add TreeStat into BEAST release
30 lines of code changed in 1 file:
Solved load issue for BEAUTi, which previously would not load without also including beast.jar
1 lines of code changed in 1 file:
Trunk: refactory xml examples
3 lines of code changed in 1 file:
(142 more)