issues
search
harmslab
/
topiary
Python framework for doing ancestral sequence reconstruction
MIT License
29
stars
6
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Update python-app.yml
#47
harmsm
closed
1 month ago
0
bug fixing
#46
harmsm
opened
1 month ago
0
Cleanup
#45
harmsm
closed
2 months ago
0
Problem with pulling proteome from NCBI--solution found!
#44
ani-sch
opened
3 months ago
3
No bootstrap MSA files written in "Alignment to Ancestors" step
#43
jmayoral1
closed
8 months ago
2
Error while running seed-to-alignment for proteins without known paralogs
#42
lbleicher
opened
1 year ago
0
Running topiary for species that are not on NCBI
#41
cyhkim
opened
1 year ago
0
Notebook fails to build on pycairo
#40
HWaymentSteele
opened
1 year ago
0
seed-to-alignment unable to retrieve proteome for key species
#39
benclifton
opened
1 year ago
1
updated for pandas 2
#38
harmsm
closed
1 year ago
0
bugfix: right response to seed species not found on ott
#37
harmsm
closed
1 year ago
0
All aditional sequences removed in seed-to-alignment step
#36
lbleicher
opened
1 year ago
8
minor bug fixes
#35
harmsm
closed
1 year ago
0
bugfix for partial md5 ncbi downloads
#34
harmsm
closed
1 year ago
0
Error in topiary-seed-to-alignment
#33
lbleicher
opened
1 year ago
25
Ncbi api key
#32
harmsm
closed
1 year ago
0
Sets entrez API key from environment
#31
odcambc
closed
1 year ago
1
Add support for Entrez.api_key
#30
odcambc
closed
1 year ago
4
fixed np.float and nfs bugs
#29
harmsm
closed
1 year ago
0
numpy 1.24 doesn't like np.float()
#28
jkaczmarski
closed
1 year ago
2
OSError: [Errno 39] Directory not empty
#27
jkaczmarski
closed
1 year ago
7
clean up to docs
#26
harmsm
closed
1 year ago
0
ready for pre-release
#25
harmsm
closed
1 year ago
0
major updates to docs
#24
harmsm
closed
1 year ago
0
Minor edits to protocol.rst
#23
Kona-O
closed
1 year ago
0
wrap chdir functions, bug fixes
#22
harmsm
closed
1 year ago
0
much improved final report code
#21
harmsm
closed
1 year ago
0
discard_key definition updated
#20
Kona-O
closed
1 year ago
0
ready for beta release
#19
harmsm
closed
1 year ago
0
Updated example seed dataset in this repo
#18
Kona-O
closed
1 year ago
1
new features
#17
harmsm
closed
1 year ago
0
intermediate commit; blocked in reports and updated mpi for cola
#16
harmsm
closed
1 year ago
0
Several updates to protocol.rst and added examples directory containing notebooks
#15
Kona-O
closed
1 year ago
0
Updated documentation
#14
harmsm
closed
2 years ago
0
Filled in docs
#13
harmsm
closed
2 years ago
0
functional reconciliation bootstrapping
#12
harmsm
closed
2 years ago
0
clean up and refactor
#11
harmsm
closed
2 years ago
0
docs updates, fixing apidoc for readthedocs
#10
harmsm
closed
2 years ago
0
Pre-release commits
#9
harmsm
closed
2 years ago
0
pre-release draft
#8
harmsm
closed
2 years ago
1
final draft of release API
#7
harmsm
closed
2 years ago
0
updated reverse blasting
#6
harmsm
closed
2 years ago
0
fixed reverse blast
#5
harmsm
closed
2 years ago
0
stitched together final pipeline architecture before submission
#4
harmsm
closed
2 years ago
0
now checks all models
#3
harmsm
closed
2 years ago
0
update test yaml
#2
harmsm
closed
2 years ago
0
now passing flake and pytest
#1
harmsm
closed
3 years ago
0