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Clonal family tree
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Where did QA255.006VH's cluster go?
#162
lauradoepker
closed
7 years ago
12
deployment on non-stoat machines?
#161
psathyrella
closed
7 years ago
2
partis shm indel positions are sometimes wrong
#160
psathyrella
closed
7 years ago
1
Annotate tree edges with AA mutations
#159
lauradoepker
closed
5 years ago
5
Frequency of leaf sequences
#158
lauradoepker
closed
7 years ago
8
Indel flagging with asterisks
#157
lauradoepker
closed
5 years ago
3
Compute time analytics
#156
metasoarous
opened
7 years ago
2
Saner parameterization of dataset generation
#155
metasoarous
closed
7 years ago
5
Better handling of clusters with fewer than 3 seqs
#154
metasoarous
closed
7 years ago
1
zero-bin to one-bin discontinuity in mutation frequencies
#153
psathyrella
closed
7 years ago
2
138 phylip processing cleanup
#152
metasoarous
closed
7 years ago
0
10 multiple timepoints
#151
metasoarous
closed
7 years ago
0
laura-mb data timepoints
#150
lauradoepker
closed
7 years ago
1
alternatives to dnapars
#149
matsen
closed
5 years ago
19
What are X's in the sequence alignment?
#148
matsen
closed
7 years ago
2
Get "Laura MB" data up and running
#147
lauradoepker
closed
7 years ago
12
ete3 tree nodes shift branch lengths
#146
krdav
closed
7 years ago
4
fix some multiple dataset related issues
#145
metasoarous
closed
7 years ago
0
123 multiple datasets
#144
metasoarous
closed
7 years ago
0
123 multiple datasets
#143
metasoarous
closed
7 years ago
0
Clean up metadata.json attribute names
#142
metasoarous
closed
7 years ago
2
122 multiple lineages
#141
metasoarous
closed
7 years ago
0
Sequence name validation
#140
metasoarous
closed
7 years ago
2
120 alternate cluster steps
#139
metasoarous
closed
7 years ago
0
Leaf names are abbreviated, I think
#138
lauradoepker
closed
7 years ago
6
Option to color nodes/branches by cluster merge step
#137
metasoarous
closed
5 years ago
2
102 parsimony
#136
wsdewitt
closed
7 years ago
0
count unpruned sequences; fixes #129; fixed #128
#135
metasoarous
closed
7 years ago
0
Add --paths-relative-to option to process_partis.py
#134
metasoarous
closed
7 years ago
0
124 display shm on tree
#133
metasoarous
closed
7 years ago
0
Highlight focus_nodes on tree
#132
metasoarous
closed
7 years ago
0
fix indel inference in ancestral reconstructions
#131
metasoarous
closed
5 years ago
11
Tree branch support
#130
matsen
closed
5 years ago
5
Display total cluster size count, pre-prune
#129
metasoarous
closed
7 years ago
0
Do sequence counts of tips, not including internal nodes
#128
metasoarous
closed
7 years ago
1
Fix DNA seq color annotations in cftweb
#127
metasoarous
closed
5 years ago
4
8 reconstructing indels
#126
metasoarous
closed
7 years ago
1
min_adcl tree trimming?
#125
metasoarous
closed
7 years ago
11
Add %SHM to leaves on trees
#124
lauradoepker
closed
7 years ago
8
Support multiple "datasets"
#123
metasoarous
closed
7 years ago
0
Multiple lineages in alignment
#122
metasoarous
closed
7 years ago
2
Add toggle for internal node names
#121
metasoarous
closed
7 years ago
1
Add links to alternate cluster steps from cluster view page
#120
metasoarous
closed
7 years ago
0
custom outdir not working
#119
wsdewitt
closed
7 years ago
1
115 naive seq
#118
metasoarous
closed
7 years ago
0
Clean up css a bit
#117
metasoarous
closed
7 years ago
0
Fix logprob indexing; fixes #114
#116
metasoarous
closed
7 years ago
0
Lineage alignment - always add naive seq and seed seq
#115
lauradoepker
closed
7 years ago
6
Logprobs are incorrect?
#114
lauradoepker
closed
7 years ago
1
Clusters for Parsimony trees are prematurely trimmed to 200 sequences
#113
lauradoepker
closed
7 years ago
3
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