rbturnbull/orthoflow
Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes.
HTMLApache-2.0
Issues
- 0
add treespaceļ¼
#88 opened - 0
allow for gz and bz2 input files.
#86 opened - 0
parallelize input validation checks
#85 opened - 0
Run test datasets on SLURM scheduler
#75 opened - 0
Add logs
#74 opened - 0
CLI info for docs
#73 opened - 0
mark temporary files for deletion
#72 opened - 1
report fail
#71 opened - 0
recreation of dag incorrect
#69 opened - 1
add_taxon.py issue
#68 opened - 0
orthofisher_hmmer_files
#67 opened - 1
- 2
user argument for bootstrapping method
#59 opened - 0
IQtree -redo behaviour
#58 opened - 0
Revert conda-lock use
#57 opened - 0
implement extract_orthofisher_scogs
#53 opened - 1
test on windows and gather issues found
#52 opened - 0
file naming conventions
#51 opened - 0
investigate disk usage efficiency
#49 opened - 0
- 1
input sources verification
#47 opened - 1
Add `input_sources` setting to config
#46 opened - 1
ortholog choice for users
#45 opened - 0
Pin conda environments
#43 opened - 5
Remove test-data from git repo
#42 opened - 3
adding quality control for alignments
#40 opened - 1
linking orthofisher to alignment module
#38 opened - 0
update names of translated cds files
#37 opened - 1
- 1
trimming step missing from workflow
#35 opened - 0
orthofisher feature
#34 opened - 2
add installation instructions to docs
#33 opened - 1
Add HTML reports to workflow
#29 opened - 1
Multiple sequences with the same taxon name in ortholog files breaks supermatrix concatenation
#28 opened - 9
Create / update test-data
#22 opened - 1
speed up filter_orthofinder.py script
#20 opened - 0
identify case studies
#19 opened - 0
Draft LaTeX doc
#17 opened - 2
choose journal
#16 opened - 0
git emoji convention?
#15 opened - 0
Add code of conduct to CONTRIBUTING.rst
#14 opened - 0
Our own executable
#13 opened - 1
reconciliation module
#12 opened - 0
gene tree module
#11 opened - 0
Fishing stream orthologs module
#10 opened - 1
sphinx plugin for reading docstrings
#9 opened - 1
supermatrix module tests
#8 opened - 1
alignment module tests
#7 opened - 1
de novo ortholog module tests
#6 opened - 1
ddrad component
#5 opened