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naturalis
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supersmart
Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
MIT License
17
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5
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Exabayes now broken on vagrant box
#60
rvosa
closed
9 years ago
6
Marker selection - be less conservative
#59
rvosa
closed
9 years ago
2
Combining subtree and backbone samples
#58
rvosa
opened
9 years ago
0
Move code out of App::Cmd classes
#57
rvosa
opened
9 years ago
8
remove all random elements
#56
hettling
opened
9 years ago
7
missing dependencies in puppet manifest
#55
rvosa
closed
9 years ago
4
Use SQLite instead of MySQL
#54
rvosa
closed
9 years ago
1
RAxML usage problems
#53
rvosa
closed
9 years ago
4
Dockerize supersmart
#52
rvosa
opened
9 years ago
10
Automatically harvest fossil calibration points
#51
rvosa
opened
9 years ago
5
Simplify logger output
#50
rvosa
closed
9 years ago
1
Simulation pipeline
#49
rvosa
closed
8 years ago
18
Multiple entries for one accession in marker table for clades
#48
hettling
closed
9 years ago
2
option to include all species in supermatrix
#47
hettling
closed
8 years ago
2
Pass root taxon to smrt taxize in command instead of via input file
#46
hettling
closed
9 years ago
1
Command to run the whole pipeline
#45
hettling
closed
9 years ago
1
Add more examples to the Installation instructions
#44
alexantonelli
closed
9 years ago
3
Warning messages from Perl (while running smrt on vagrant)
#43
alexantonelli
closed
9 years ago
2
Backbone tree bootstrap
#42
hettling
closed
9 years ago
3
publish provisioned VM in Vagrant cloud
#41
hettling
closed
9 years ago
16
exemplar species has markers for backbone but no markers for clade
#40
hettling
closed
9 years ago
1
Exemplars assigned to the wrong clades
#39
hettling
closed
9 years ago
1
Example OneZoom image of Primates
#38
rvosa
closed
8 years ago
10
taxize fails
#37
rvosa
closed
9 years ago
1
App::Cmd not being installed
#36
rvosa
closed
9 years ago
3
remove redundant columns in supermatrix
#35
hettling
closed
9 years ago
1
Ambiguity in alignment file names
#34
hettling
closed
9 years ago
1
Tag with version number
#33
rvosa
closed
9 years ago
1
very long branches in backbone tree
#32
hettling
closed
9 years ago
1
Website enhancements
#31
rvosa
closed
9 years ago
7
outgroup rooting
#30
rvosa
closed
9 years ago
7
Specify taxonomic expansion on the command line
#29
rvosa
closed
9 years ago
0
some node IDs don't end up in common tree
#28
rvosa
closed
9 years ago
4
add script to PATH on virtual machine to open configuration file
#27
hettling
closed
9 years ago
3
locations for names and fossil files should not be hard-coded in 'run' script
#26
hettling
closed
9 years ago
1
Possibility to run the pipeline from any directory on the VM
#25
hettling
closed
9 years ago
2
Allow non-root installs
#24
rvosa
closed
9 years ago
3
Filter on certain annotation values
#23
rvosa
opened
9 years ago
1
Vagrant and diacritical user names
#22
rvosa
closed
9 years ago
1
Possibility of enforcing taxa to be present in backbone tree
#21
alexantonelli
closed
9 years ago
1
Quite a lot of unit tests are failing
#20
rvosa
closed
9 years ago
4
Create a new folder to create a new phylogeny
#19
FabienCondamine
closed
10 years ago
1
Bug issues for installation
#18
FabienCondamine
closed
10 years ago
3
Bug issue for the building of Primate phylogeny
#17
FabienCondamine
closed
10 years ago
6
User can specify lowest taxonomic level to be included in trees
#16
alexantonelli
closed
9 years ago
2
User can provide more than 1 'root taxon' to be expanded
#15
alexantonelli
closed
10 years ago
1
Create a StorageService
#14
rvosa
closed
9 years ago
2
Create a ParallelizationService
#13
rvosa
closed
10 years ago
2
Bayesian estimation of genus-level trees (for future versions)
#12
alexantonelli
closed
10 years ago
3
Delete abandoned scripts
#11
rvosa
closed
10 years ago
0
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