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matsen
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pplacer
Phylogenetic placement and downstream analysis
http://matsen.fredhutch.org/pplacer/
GNU General Public License v3.0
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Merging via intersection for hybrids, and lots of noisy errors if sequence file and jplace are different.
#333
matsen
closed
10 years ago
0
318 placement specific mask
#332
matsen
closed
10 years ago
0
Invalid number when parsing JSON ouput
#331
gjospin
closed
10 years ago
11
Stack overflow error
#330
crosenth
closed
6 years ago
7
by_taxa output of classif_table.py should be ordered by freq/tally
#329
metasoarous
opened
10 years ago
1
loss of specificity in 318-placement-specific-mask branch
#328
nhoffman
closed
10 years ago
1
guppy classify (hybrid2) should ignore sequences not in jplace
#327
nhoffman
closed
10 years ago
3
Feature request: create directory specified by 'guppy lpca --out-dir' if it doesn't already exist
#326
nhoffman
opened
10 years ago
0
324 deduplicate seqs compression
#325
nhoffman
closed
11 years ago
0
file compression support for deduplicate_sequences.py
#324
nhoffman
closed
11 years ago
1
read compressed alignment files?
#323
nhoffman
closed
11 years ago
9
Move to Batteries 2.1.0 / OCaml 4.01.0
#322
cmccoy
closed
10 years ago
3
Clarify OCaml 3.12.1 requirement
#321
cmccoy
closed
11 years ago
2
batteries.2.0.0 installation fails
#320
nhoffman
closed
11 years ago
3
Specifying --write-pre-masked shouldn't prevent placement
#319
metasoarous
closed
11 years ago
5
Use query-specific mask for first stage of optimization.
#318
matsen
closed
10 years ago
0
pplacer should respect --out-dir when using --write-masked
#317
metasoarous
closed
10 years ago
0
pplacer should warn rather than die if an alignment looks like nt.
#316
matsen
closed
11 years ago
0
`rppr info` chokes on packages that don't have a taxonomy.
#315
matsen
closed
11 years ago
1
have `-help` spit out a link to online docs
#314
matsen
opened
11 years ago
2
Make an option for only masking columns that are also gap in all reads
#313
matsen
closed
10 years ago
1
Clarify descriptions of `--normalize-by-specimen` flag functionality in scripts/classif_rect.py
#312
metasoarous
closed
10 years ago
8
Support Infernal 1.1 in `refpkg_align.py`
#311
cmccoy
opened
11 years ago
0
More elegant failure with faulty place files
#310
matsen
opened
11 years ago
2
Wrapping up ePCA SOM implementation
#309
matsen
closed
11 years ago
0
add something to FAQ explaining why pplacer does not output a newick tree
#308
matsen
closed
11 years ago
0
Change AWPD to BWPD
#307
cmccoy
closed
11 years ago
1
make random tie breaking the default for NBC.
#306
matsen
closed
11 years ago
0
fix cdd compiler warnings
#305
matsen
closed
11 years ago
1
cache NBC word counts?
#304
nhoffman
closed
11 years ago
2
Move to Batteries 2.0
#303
cmccoy
closed
11 years ago
0
implementation of guppy length pca
#302
bcclaywell
closed
11 years ago
1
guppy compile fail
#301
hexaquo
closed
11 years ago
3
'guppy classify --classifier nbc': unaligned sequences cause error without --no-pre-mask
#300
nhoffman
closed
11 years ago
3
NAN likelihoods when using emperical frequencies and a state is never seen
#299
matsen
closed
11 years ago
0
Speed up Three_tax.find_upper_limit
#298
cmccoy
closed
11 years ago
0
Multicore squash bootstrapping
#297
cmccoy
closed
11 years ago
0
Guppy merge 's tree comparison
#296
gjospin
closed
11 years ago
1
Add `--unitize` option to guppy squash
#295
cmccoy
closed
11 years ago
0
Approximate likelihood-curve fitting using non-linear least squares
#294
cmccoy
opened
11 years ago
0
Switch build to OPAM
#293
cmccoy
closed
11 years ago
0
Failing build
#292
CosteaPaul
closed
11 years ago
9
Add qD(T) and qPD(T) to `guppy fpd`
#291
cmccoy
closed
11 years ago
0
randomly break ties for NBC
#290
matsen
closed
11 years ago
1
Documentation is 404
#289
xapple
closed
12 years ago
1
add `guppy placemat`
#288
habnabit
closed
11 years ago
0
Uninformative error when reference and query sequence IDs overlap
#287
cmccoy
closed
12 years ago
0
Removal of files created by --mmap-file
#286
koadman
closed
12 years ago
1
taxtastic-0.4.0 installation error
#285
koadman
closed
12 years ago
2
taxit taxtable error
#284
koadman
closed
12 years ago
2
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