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matsengrp
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cft
Clonal family tree
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Run reconstructions for clusters containing seeds (or other sequences of interest) in unseeded partitions
#212
metasoarous
closed
6 years ago
0
Resolve issue with only largest cluster processing for each unseeded partition
#211
metasoarous
closed
6 years ago
0
Adapt CFTWeb for unseeded partitions
#210
metasoarous
closed
6 years ago
1
Table filtering
#209
metasoarous
closed
5 years ago
1
Table sorting
#208
metasoarous
closed
5 years ago
1
refine "click through" routing for when (e.g.) a partition just has one cluster
#207
metasoarous
closed
6 years ago
0
by_subject view should have separate seeded and unseeded tables
#206
metasoarous
closed
6 years ago
0
Adapt CFTWeb interface to new schema to account for addition of the `reconstruction` entities
#205
metasoarous
closed
6 years ago
1
Refactor cft to handle unseeded partitions
#204
metasoarous
closed
6 years ago
0
Duplicity -> multiplicity
#203
metasoarous
closed
6 years ago
0
Review/fix rerooting procedure
#202
metasoarous
closed
6 years ago
3
Freeze updated dataset for Laura
#201
metasoarous
closed
6 years ago
1
Add Newick file download
#200
lauradoepker
closed
6 years ago
2
Improve performance for by subject pages
#199
metasoarous
closed
7 years ago
1
189 septmpts tmpt assignment fix
#198
metasoarous
closed
7 years ago
0
Plot duplicity legend with pie charts instead of circle face so sizes…
#197
metasoarous
closed
7 years ago
0
Fix duplicity scale
#196
metasoarous
closed
7 years ago
0
Don't allow any stop codons; fixes #193
#195
metasoarous
closed
7 years ago
0
Make sure asr depends on input tree file in SConstruct, and add check…
#194
metasoarous
closed
7 years ago
0
Disallow stop codons for our CFT trees
#193
lauradoepker
closed
7 years ago
1
Problem with dnaml sequence name trimming reversal
#192
metasoarous
closed
7 years ago
2
minadcl tree problems
#191
lauradoepker
closed
7 years ago
3
Broken cluster steps or cluster siblings
#190
metasoarous
closed
7 years ago
2
Issues with unmerged timepoint runs showing multiple timepoints
#189
metasoarous
closed
7 years ago
0
Choosing which antibodies to make from non-seeded clusters
#188
psathyrella
opened
7 years ago
7
increase width of trees on CFTweb
#187
lauradoepker
closed
6 years ago
1
Identify leaf sequences that have highest sequence identity to each internal node (i.e. lineage member)
#186
lauradoepker
closed
4 years ago
20
Download link for fastas for all sequences and lineage
#185
lauradoepker
closed
7 years ago
1
12 pruning
#184
wsdewitt
closed
7 years ago
5
Only perform clustering steps if fewer than ____ sequences in "clustering step 0"
#183
lauradoepker
closed
7 years ago
5
Refinement of minadcl?
#182
metasoarous
closed
5 years ago
6
Methods (and dataflow for Laura's education)
#181
lauradoepker
closed
6 years ago
4
Keep all seeds when pruning and minadcl thinning
#180
lauradoepker
closed
6 years ago
17
revisit subsampling?
#179
matsen
closed
6 years ago
9
CFT reformat for non-seed partitions
#178
lauradoepker
closed
6 years ago
2
How to filter sequences
#177
matsen
closed
7 years ago
16
smarter selection of parsimony tree
#176
wsdewitt
closed
5 years ago
8
Alignment overview
#175
matsen
closed
5 years ago
5
Download dataset feature
#174
metasoarous
closed
6 years ago
2
125 min adcl tree trimming
#173
metasoarous
closed
7 years ago
0
Improve regular pruning strategy
#172
metasoarous
closed
5 years ago
4
Immortalize these trees for publication
#171
lauradoepker
closed
7 years ago
14
replace default tree building program (dnaml) with raxml-ng
#170
metasoarous
closed
4 years ago
41
155 parameterize datasets
#169
metasoarous
closed
7 years ago
0
Sequence names changed?
#168
lauradoepker
closed
7 years ago
17
RDF data model
#167
metasoarous
closed
7 years ago
11
Generalize cft and cftweb
#166
metasoarous
closed
6 years ago
2
Is there a way to toggle between different timepoints on the trees?
#165
lauradoepker
closed
7 years ago
9
Dot labeling for different antibody clusters
#164
lauradoepker
closed
5 years ago
2
Can we change the dots/key for the seed sequences on the trees?
#163
lauradoepker
closed
7 years ago
5
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