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Commits : Listings

Analyzed about 6 hours ago. based on code collected about 21 hours ago.
Jun 16, 2023 — Jun 16, 2024
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
removing old species tree
Rutger Vos
More... over 12 years ago
adding renamed species tree
Rutger Vos
More... over 12 years ago
Merge github.com:ncbnaturalis/cobra
Rutger Vos
More... over 12 years ago
Have now run all un-commented targets
Rutger Vos
More... over 12 years ago
The MRP matrices from TreeBASE now also use the CODES instead of the NCBI taxon identifiers as row labels.
Rutger Vos
More... over 12 years ago
The MRP matrix for the NCBI common tree now also uses the CODES instead of the NCBI taxon identifiers as row labels.
Rutger Vos
More... over 12 years ago
We no longer use the $map to go from NCBI taxon IDs to binomials. Instead we simply use the CODE labels from the MRP matrices unchanged.
Rutger Vos
More... over 12 years ago
Now only the CODE, not the scientific name, is embedded in the phyloxml. This is because multiple subspecies map onto the same code, so archeopteryx might get confused otherwise.
Rutger Vos
More... over 12 years ago
Now only the CODE, not the scientific name, is embedded in the phyloxml. This is because multiple subspecies map onto the same code, so archeopteryx might get confused otherwise.
Rutger Vos
More... over 12 years ago
The NCBI common tree is now written out as a constraint tree with CODES as tip names. Because the NCBI common tree had some subspecies that map onto the same CODE we now need to prune these out. In actuality this is only the case for CROTDURI.
Rutger Vos
More... over 12 years ago
Now tests to see if file has been written (rather than purl has been seen), this so that we can restart it.
Rutger Vos
More... over 12 years ago
adding additional reference material on CRISP evolution
Rutger Vos
More... over 12 years ago
adding test script for ncbi common tree integrity
Rutger Vos
More... over 12 years ago
only one polytomy this time: (CELEWARR:1.000000,GERRINFE:1.000000,PSEUAPOD:1.000000):1.000000;
Rutger Vos
More... over 12 years ago
re-ran supertree analysis
Rutger Vos
More... over 12 years ago
re-generated phyloxml files
Rutger Vos
More... over 12 years ago
ran SDI on command line
Rutger Vos
More... over 12 years ago
re-generated MRP matrices from source trees
Rutger Vos
More... over 12 years ago
re-downloaded source trees from TreeBASE
Rutger Vos
More... over 12 years ago
generated MRP matrices from additional, newly downloaded source trees
Rutger Vos
More... over 12 years ago
found more source trees on TreeBASE
Rutger Vos
More... over 12 years ago
newly downloaded from ncbi
Rutger Vos
More... over 12 years ago
This test script checks to see that taxa.csv follows our cardinality rules.
Rutger Vos
More... over 12 years ago
NCBI is OK with us only sleeping for 2 seconds.
Rutger Vos
More... over 12 years ago
Fixed all incorrect mappings identified by t/taxamap.t, ensured consistency using t/speciescodes.t
Rutger Vos
More... over 12 years ago
Added link to bioperl-live
Rutger Vos
More... over 12 years ago
added link to paper on organizing comp bio projects
Rutger Vos
More... over 12 years ago
Update README
Rutger Vos
More... over 12 years ago
adding manually pruned version of crisp alignment
Rutger Vos
More... over 12 years ago
updated project file
Rutger Vos
More... over 12 years ago