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yatisht
/
usher
Ultrafast Sample Placement on Existing Trees
MIT License
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BUG: Web usher sometimes crashes with `menuparent" id="myData">My Data`
#230
corneliusroemer
opened
2 years ago
0
Small pull request including bugfix and JSON filtering
#229
jmcbroome
closed
2 years ago
0
ENH: Make `sample type` an Auspice filter
#228
corneliusroemer
opened
2 years ago
7
BUG: Don't get result when uploading about 240 sequences, some of them with spaces in fasta header, e.g. `Czech Republic`
#227
corneliusroemer
opened
2 years ago
1
keep protobuf generation in sync
#226
yceh
closed
2 years ago
0
fix centos build?
#225
yceh
closed
2 years ago
0
cannot install
#224
lpipes
closed
2 years ago
22
Do radius doubling on final round of optimization
#223
yceh
closed
2 years ago
2
BUG: Multiple mutations in one codon cause can cause false amino acid mutation
#222
corneliusroemer
closed
1 year ago
4
ENH: allow placement of sequence fragments shorter than 10k bp
#221
corneliusroemer
closed
1 year ago
1
New matUtils Features
#220
jmcbroome
closed
2 years ago
1
matOptimize crashes when samples are numerically named
#219
Danderson123
closed
1 year ago
1
Add option to output closest relative(s) per sample
#218
amkram
closed
2 years ago
0
matOptimize crashes with small vcf input
#217
willdumm
closed
1 year ago
3
Add option to include nt mutations in taxonium export
#216
amkram
closed
2 years ago
1
Root-To-Tip Distance or Path?
#215
ktmeaton
closed
2 years ago
4
Usher matoptimize fuse
#214
yceh
closed
2 years ago
5
Usher matoptimize fuse
#213
yceh
closed
2 years ago
0
Issue with a Delta sub lineage
#212
shay671
closed
1 year ago
4
Path issues with matUtils extract
#211
theosanderson
closed
2 years ago
4
ENH: Display all maximally parsimonious locations in web interface, not just 1
#210
corneliusroemer
opened
2 years ago
4
usher: undefined symbol: _ZN5boost9iostreams4zlib8deflatedE
#209
jwni2018
closed
2 years ago
5
Fix vcf importer
#208
yceh
closed
2 years ago
0
Recommended way to visualize a huge mutation-annotated tree?
#207
fritzo
closed
2 years ago
2
Not all nodes are shown in the tsv file generated by the function --translate
#206
akograf
closed
1 year ago
4
Problem with UShER web server - unbalanced parenthesis warning/error
#205
flashton2003
closed
2 years ago
8
a split in the BA.3 tree
#204
shay671
closed
2 years ago
2
Ripples optimization again
#203
yceh
closed
2 years ago
1
faster Ripples
#202
yceh
closed
2 years ago
1
Conda local build instructions fail on Ubuntu
#201
jmcbroome
closed
2 years ago
2
Modularized VCF reading into MAT namespace
#200
kvargha
closed
2 years ago
1
Update Nextstrain clades to include 21K (Omicron)
#199
corneliusroemer
closed
2 years ago
2
Whitelist in matUtils extract + refactoring of introduce
#198
jmcbroome
closed
2 years ago
0
new matUtils pruning option + efficiency and clarity refactoring
#197
jmcbroome
closed
2 years ago
2
[Enhancement] Don't delete trees or allow manual 'save' so that links don't break after few weeks
#196
corneliusroemer
opened
2 years ago
1
Modularized VCF reading
#195
kvargha
closed
2 years ago
1
switch back to openmpi
#194
yceh
closed
2 years ago
0
Query about summarising mutation information with matUtils
#193
charlesfoster
closed
2 years ago
4
Use isa-l for decompression
#192
yceh
closed
2 years ago
1
--write-taxodium ouput changes for other pathogens
#191
amkram
closed
2 years ago
1
New masking functionality, bugfixes
#190
jmcbroome
closed
2 years ago
3
[Enhancement] List assigned pango lineage for uploaded samples as coloring on Auspice tree
#189
corneliusroemer
opened
2 years ago
2
Cap buffer size
#188
yceh
closed
2 years ago
0
Update README.md
#187
abschneider
closed
2 years ago
0
Impute deletions as well as substitutions?
#186
fritzo
opened
2 years ago
1
Update snakemake workflow
#185
abschneider
closed
2 years ago
0
Bugfix and pruning direction to search
#184
yceh
closed
2 years ago
0
matUtils annotate: Added option --clade-mutations (-M) for specifying clades by sets of mutations
#183
AngieHinrichs
closed
2 years ago
0
matUtils extract --write-taxodium: nuc mutations
#182
AngieHinrichs
closed
2 years ago
3
update snakefile
#181
abschneider
closed
2 years ago
0
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