yatisht usher issues - Githubissues

yatisht / usher

Ultrafast Sample Placement on Existing Trees

MIT License

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issues

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NC_045512 shows up in MAT when extracting from a WNV auspice tree

#378 jcw349 opened 1 day ago
3
Add --anchor-samples option to add specific sequences to subtrees

#377 AngieHinrichs closed 1 month ago
0
does `matUtils extract` has `-M` function?

#376 liamxg opened 1 month ago
3
what is the `cluster_span` meaning?

#375 liamxg opened 1 month ago
1
Several attempts at installation fail

#374 terrycojones opened 2 months ago
4
Usher crashing when uploading any amount of data

#373 corneliusroemer closed 3 months ago
2
SC2 tree: Branch specific masking for nuc 21941 (S:127) on BA.2.86 branch

#372 corneliusroemer opened 3 months ago
0
Fix auspice radial and unrooted views

#371 aofarrel closed 1 month ago
0
Docker image uses an old version of `sed` that doesn't work properly within Docker

#370 aofarrel opened 3 months ago
0
Mac OS installation script seems broken

#369 aofarrel opened 4 months ago
0
Duplicate Nodes with Special Characters in Name

#368 gp201 opened 4 months ago
1
Extracting gene mutations using matUtils extract and generate subsequent tree

#367 Biophylo2001 opened 4 months ago
1
USher: have been mutations displayed on the branch changed? or is it a bug ?

#366 FedeGueli opened 4 months ago
12
matutils extract segfaults with -s, but not -K, if no samples in text file are on tree

#365 aofarrel opened 4 months ago
1
Identify amino acid mutation spread in large population

#364 Biophylo2001 opened 4 months ago
0
Usher server down: "Very early error"

#363 corneliusroemer opened 4 months ago
6
Apple M1 arm64 How to install USHER

#362 Lijuming33 opened 5 months ago
0
no response after I upload 1400 sequences.

#361 liamxg opened 6 months ago
12
Ignore

#360 corneliusroemer closed 7 months ago
0
Create CODE_OF_CONDUCT.md

#359 russcd closed 7 months ago
0
Too many sequences in an output tree

#358 imdanique opened 7 months ago
1
matUtils updates: new subcommand "fix"; improvements to MAT::Tree:move_node and mask --move-nodes

#357 AngieHinrichs closed 8 months ago
0
Different number of Sequences in Tree and Fasta

#356 wtporter opened 8 months ago
2
fix missing root in fixed tree search

#355 yceh closed 8 months ago
0
Unclear why reversion is not indicated in Auspice export

#354 corneliusroemer opened 8 months ago
2
Very early error: Couldn't connect to database hgcentral on hgnfs1 as hgcentuser. Too many connections

#353 corneliusroemer opened 8 months ago
1
Suggestion to update removal rules to adapt to the current mass recombinant situation

#352 aviczhl2 opened 9 months ago
0
Error `needLargeMem: Out of memory - request size 65568 bytes, errno: 12`

#351 corneliusroemer opened 9 months ago
13
Issues in XBB.1.9* cluster

#350 NkRMnZr opened 10 months ago
0
ENH: Store imputed nucleotides for each tip

#349 corneliusroemer opened 11 months ago
0
several issues

#348 shay671 opened 11 months ago
1
ENH: Quick way to get Auspice/Nextstrain subtree by uploading a single EPI ISL

#347 corneliusroemer opened 11 months ago
2
Cannot analyze XBB.1.5+T10204C samples

#346 Over-There-Is closed 12 months ago
1
several issues

#345 shay671 opened 1 year ago
2
2 lineage issues

#344 shay671 opened 1 year ago
1
filter epps if they are clustered around a single node

#343 yceh closed 1 year ago
0
Add option (-E) in matoptimize to output the number of EPPs in the branch length field of newick

#342 yceh closed 1 year ago
0
Show more context samples in downsampled tree, max out 5k sequences

#341 corneliusroemer opened 1 year ago
0
Whole tree mode for Usher

#340 aviczhl2 opened 1 year ago
1
public tree: Apostrophes in clade names

#339 theosanderson closed 1 year ago
4
fix computing root mutation

#338 yceh closed 1 year ago
0
Adding Genbase sequences to usher

#337 aviczhl2 closed 1 year ago
6
getting non-coding mutations using `matUtils summary --translate`

#336 jbloom opened 1 year ago
3
Remove or rename "pangoLEARN" lineage column

#335 corneliusroemer opened 1 year ago
0
automatically disable optimization if ref contain ambiguous nucleotide

#334 yceh closed 1 year ago
4
Easily extract metadata for node ID of interest identified through ripples + general usage query

#333 charlesfoster closed 1 year ago
3
Exclude sequences that contain `/env/`

#332 corneliusroemer opened 1 year ago
0
Fix subtree extraction when requested size is greater than the number of leaves

#331 yceh closed 1 year ago
0
`Warning/Error(s): Missing file subtree-1-mutations.txt in usher results` when uploading mpox sequences

#330 corneliusroemer opened 1 year ago
4
--haplotype rework and metadata loading flag

#329 jmcbroome closed 1 year ago
0