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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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unit tests for PCA broken
#283
matsen
closed
12 years ago
0
Support inflation parameter in `guppy mcl`
#282
cmccoy
closed
12 years ago
2
Option to multiply by left by length diagonal matrix in epca
#281
metasoarous
opened
12 years ago
0
pplacer without a reference package fails without an explicitly-provided reference alignment
#280
habnabit
closed
12 years ago
0
broken links in documentation
#279
cmccoy
closed
12 years ago
1
Support split placefiles in `guppy rarefact`
#278
cmccoy
closed
12 years ago
2
add multivariate hypergeometric sampling to `guppy rarefy`
#277
habnabit
closed
12 years ago
0
add `-k` for maximum k to `guppy rarefact`
#276
habnabit
closed
12 years ago
0
Allow `guppy rarefy` to use pquery multiplicity
#275
matsen
closed
12 years ago
2
Allow `guppy rarefact` to use pquery multiplicity
#274
habnabit
closed
12 years ago
0
fix convexify for multifurcating trees
#273
matsen
closed
11 years ago
0
add `rppr confusion`
#272
habnabit
opened
12 years ago
2
flesh out ADCL documentation and link to arxiv
#271
matsen
opened
12 years ago
0
should we be telling people to source install_pplacer.sh?
#270
matsen
closed
12 years ago
3
try doing only approximate PAM
#269
matsen
closed
12 years ago
1
`--map-rejection` for pplacer
#268
habnabit
closed
12 years ago
2
add tax_id counts to rppr convex_taxids
#267
habnabit
closed
12 years ago
0
add map_{ratio,overlap} to guppy to_csv
#266
habnabit
closed
12 years ago
0
`rppr reroot` can give suboptimal roots in some situations with unclassified sequences
#265
habnabit
closed
12 years ago
0
link back to pplacer binary downloads from docs
#264
matsen
closed
12 years ago
1
Newick_gtree.prune_to_pql can put placements on the root edge
#263
habnabit
closed
12 years ago
0
PP integration fails with zero branch lengths
#262
matsen
closed
12 years ago
0
add `rppr convex_taxids`
#261
habnabit
closed
12 years ago
0
add rarefaction of phylogenetic diversity
#260
habnabit
closed
12 years ago
0
add `guppy mcl`
#259
habnabit
closed
12 years ago
2
diplac -> adcl
#258
matsen
closed
12 years ago
2
s/voronoi/min_adcl/ and s/vorotree/adcltree/
#257
matsen
closed
12 years ago
0
allow pplacer to mmap instead of doing large allocations
#256
habnabit
closed
12 years ago
4
add `guppy to_csv`
#255
habnabit
closed
12 years ago
2
add note about n_keep and n_pitches to FAQ
#254
matsen
opened
12 years ago
0
Print all placement names in `guppy diplac`
#253
cmccoy
closed
12 years ago
0
add --all-alternates to `rppr convexify`
#252
habnabit
closed
12 years ago
0
hybrid5-- no big jumps in taxonomic hierarchy
#251
matsen
closed
12 years ago
0
have to_rdp be able to export to mothur-acceptable format
#250
matsen
closed
12 years ago
0
`guppy rarefy`
#249
matsen
closed
12 years ago
0
add pre-masking to nbc classifier
#248
matsen
closed
12 years ago
1
(re)add `guppy unifrac`
#247
habnabit
closed
12 years ago
0
Add `--always-include` flag to `rppr voronoi` and `vorotree`
#246
cmccoy
closed
12 years ago
0
Allow reference packages to be read from zip files
#245
habnabit
closed
12 years ago
0
`rppr infer` fails if a classification can't be found for a sequence
#244
habnabit
closed
12 years ago
0
`rppr reroot` fails when sequences are missing taxonomy
#243
cmccoy
closed
12 years ago
0
--max-adcl flag for voronoi
#242
matsen
closed
12 years ago
0
--target-rank changes
#241
matsen
closed
12 years ago
0
Add `-o` flag to pplacer
#240
cmccoy
closed
12 years ago
0
Minimize ADCL using PAM
#239
cmccoy
closed
12 years ago
0
Prefiltering of constant edges for edgePCA
#238
metasoarous
closed
12 years ago
1
add a multiplicity column to diplac
#237
matsen
closed
12 years ago
1
Numeric taxon labels parsed as confidence values
#236
cmccoy
closed
12 years ago
0
--rep-edges for splitify subcommand
#235
matsen
closed
12 years ago
4
guppy fat sets many branch lengths to 0.01
#234
joelb123
closed
12 years ago
3
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