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dermestid
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bold-phylodiv-scripts
Scripts to calculate phylodiversity and its distribution from BOLD DNA barcode data.
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Only plot species data in grid squares with PD
#92
dermestid
closed
3 years ago
0
Display difference of PD and species count
#91
dermestid
closed
3 years ago
0
Separate out easily-deployable web components
#90
dermestid
closed
3 years ago
0
Use server-sent events for long-running tasks
#89
dermestid
closed
3 years ago
1
Separate out easily-deployable web components
#88
dermestid
closed
3 years ago
0
Calculate and plot species counts alongside tree length
#87
dermestid
closed
3 years ago
0
Calibrate colouring of PD
#86
dermestid
closed
3 years ago
1
More control over plotting
#85
dermestid
closed
3 years ago
1
More and better status messages
#84
dermestid
closed
3 years ago
1
Leaflet map of PD
#83
dermestid
closed
3 years ago
0
Leaflet maps
#82
dermestid
closed
3 years ago
0
added interface page, fixed some exit messages
#81
dermestid
closed
3 years ago
0
AJAX-type interface
#80
dermestid
closed
3 years ago
0
Outputs JSON result and status messages
#79
dermestid
closed
3 years ago
0
Invalid taxon is not downloaded
#78
dermestid
closed
3 years ago
0
Invalid taxon results in lots of (all?) sequences being downloaded
#77
dermestid
closed
3 years ago
0
PAUP output piped without need for files
#76
dermestid
closed
3 years ago
0
Removed replication code
#75
dermestid
closed
3 years ago
0
Remove replication code from phylodiv.php
#74
dermestid
closed
3 years ago
0
Replication of subsampling etc in parallel
#73
dermestid
closed
3 years ago
1
Update readme for web server usage
#72
dermestid
opened
3 years ago
1
Able to run on a web server
#71
dermestid
closed
3 years ago
0
Pipe PAUP
#70
dermestid
closed
3 years ago
1
Different means or format of output
#69
dermestid
closed
3 years ago
0
Get it to run on a web server
#68
dermestid
closed
3 years ago
0
Parallelized alignment
#67
dermestid
closed
3 years ago
0
Reduced download progress update to single line
#66
dermestid
closed
3 years ago
0
Created trees aren't renamed
#65
dermestid
closed
3 years ago
0
Terminology fixed
#64
dermestid
closed
3 years ago
1
Don't rename created trees
#63
dermestid
closed
3 years ago
0
Directory restructure
#62
dermestid
closed
3 years ago
0
Directory structure
#61
dermestid
closed
3 years ago
0
Reduced verbosity of console output
#60
dermestid
closed
3 years ago
0
Changed fn geo_divide() to Division_Scheme::sort()
#59
dermestid
closed
3 years ago
0
Moved various setup code to new files
#58
dermestid
closed
3 years ago
0
Google maps integration
#57
dermestid
closed
3 years ago
1
Do rarefaction/extrapolation of sample size for PD
#56
dermestid
opened
3 years ago
1
Do alignment in parallel
#55
dermestid
closed
3 years ago
2
Moved some data file functionality to new classes
#54
dermestid
closed
3 years ago
0
Output division scheme to results file
#53
dermestid
closed
3 years ago
0
Estimate map coordinates from other location data available in BOLD
#52
dermestid
opened
3 years ago
0
Any files used by script should be in the temp folder while it's running
#51
dermestid
closed
3 years ago
1
Output division scheme to results file
#50
dermestid
closed
3 years ago
0
Different approaches to geographical subsampling
#49
dermestid
opened
3 years ago
3
Skip broken entries in BOLD output
#48
dermestid
closed
3 years ago
0
Skip broken entries in BOLD output
#47
dermestid
closed
3 years ago
0
PAUP freezes on quit for a large input file
#46
dermestid
closed
3 years ago
2
Sometimes BOLD output is not in expected format
#45
dermestid
opened
3 years ago
1
Command line arguments for coord grid size read
#44
dermestid
closed
3 years ago
0
geo_divide saves total_sequence_count
#43
dermestid
closed
3 years ago
0
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