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McTavishLab
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physcraper
Welcome to Physcraper’s repository! Automatic gene tree updating using the Open Tree of Life.
https://physcraper.readthedocs.io/en/main/
GNU General Public License v3.0
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biopython error
#183
lskatz
opened
1 year ago
0
KeyError: '^ot:ottId'
#182
LunaSare
opened
2 years ago
0
error with search_taxon ott:417957
#181
LunaSare
closed
2 years ago
2
Clean code
#180
snacktavish
closed
3 years ago
0
undefined character
#179
jtfield
closed
2 years ago
3
output - file with taxon names that are all gaps in input alignment
#178
LunaSare
opened
3 years ago
1
documenttaion - add docker to install instructions
#177
LunaSare
opened
3 years ago
1
add jupyter notebook to dockerfile
#176
LunaSare
opened
3 years ago
3
Write implementation section as md
#175
LunaSare
opened
3 years ago
0
Add a Troubleshooting page
#174
LunaSare
opened
3 years ago
0
automatically generate a file with all citations
#173
LunaSare
opened
3 years ago
0
reviewer 2 - comment 8 - check internal links in docs
#172
LunaSare
closed
3 years ago
1
reviewer 2 - comment 7 - explain polytomy handling in docs
#171
LunaSare
closed
3 years ago
1
reviewer 2 - comment 6 - tree relabelling
#170
LunaSare
closed
3 years ago
1
reviewer 2 - comment 5 - clarify mapping is automatic
#169
LunaSare
closed
3 years ago
1
reviewer 2 - comment 4 - orthologs instead of homologs
#168
LunaSare
closed
3 years ago
0
reviewer 2 - comment 3 - clarify expectations for users
#167
LunaSare
closed
3 years ago
1
reviewer 2 - comment 2 - clarify differences with existing tools
#166
LunaSare
closed
3 years ago
1
reviewer 2 - comment 1 - clarify usability
#165
LunaSare
closed
3 years ago
2
Clean docs
#164
LunaSare
closed
3 years ago
0
Lint
#163
snacktavish
closed
3 years ago
1
Reqs update
#162
snacktavish
closed
3 years ago
0
Ejm ms rev
#161
snacktavish
closed
3 years ago
1
duplicated taxon names on input alignment file "taxonname.fas"
#160
LunaSare
closed
3 years ago
1
Cleanup
#159
LunaSare
closed
3 years ago
1
homogenize terms across docs
#158
LunaSare
closed
3 years ago
1
add physcraper citation to readme and credits on docs
#157
LunaSare
closed
3 years ago
1
double 'example commands' section on physcraper run docs needs merging
#156
LunaSare
closed
3 years ago
1
reviewer 1 - minor comments
#155
LunaSare
closed
3 years ago
1
reviewer 1 - comment 7 - aminoacid alignments
#154
LunaSare
opened
3 years ago
1
reviewer 1 - comment 2 - things labeled as "under construction"
#153
LunaSare
closed
3 years ago
4
reviewer 1 - comment 1 - missing things on readme
#152
LunaSare
closed
3 years ago
2
toc not showing on readthedocs, only on local build
#151
LunaSare
closed
3 years ago
2
Supertreebasefix
#150
snacktavish
closed
3 years ago
1
Pyopensci rev
#149
snacktavish
closed
3 years ago
0
Reqs update
#148
snacktavish
closed
3 years ago
0
reviewer 1 - comment 8 - Error on treebase tree
#147
snacktavish
closed
3 years ago
3
reviwer 1 - comment 6 - Progress bar for blast runs
#146
snacktavish
opened
3 years ago
1
reviewer 1 - comment 5 - function documentation
#145
snacktavish
closed
3 years ago
1
reviewer 1 - comment 4 - alternative alignment options
#144
snacktavish
closed
3 years ago
1
reviewer 1 - comment 3 - Anaconda/virtualenv
#143
snacktavish
closed
3 years ago
2
Pylint
#142
snacktavish
closed
4 years ago
0
Docs
#141
snacktavish
closed
4 years ago
0
Update location of instructions when blast db is old
#140
snacktavish
closed
3 years ago
1
No ingroup fix
#139
snacktavish
closed
4 years ago
1
Tree not found?
#138
mkandziora
opened
4 years ago
2
ot_ws_wrapper NoneType
#137
mkandziora
opened
4 years ago
3
add do_not_align option
#136
snacktavish
opened
4 years ago
0
Pylint
#135
snacktavish
closed
4 years ago
0
fix write info bug
#134
snacktavish
closed
4 years ago
0
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