matsen pplacer issues - Githubissues

matsen / pplacer

Phylogenetic placement and downstream analysis

http://matsen.fredhutch.org/pplacer/

GNU General Public License v3.0

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issues

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comments for every non-trivial function

#183 matsen closed 12 years ago
0
weighted -> spread and unweighted -> point

#182 matsen closed 13 years ago
1
Have mft be able to invert the effect of copy number

#181 matsen closed 12 years ago
2
refpkg_align.py is broken

#180 cmccoy closed 12 years ago
1
would like to use %g for json output of floats

#179 matsen closed 13 years ago
0
guppy compress chokes on trees without a root branch length

#178 matsen closed 13 years ago
0
make --multip-gt option for guppy filter

#177 matsen closed 13 years ago
0
`rppr reroot` fails with Invalid_argument

#176 cmccoy closed 13 years ago
0
occupied_rates need a fix

#175 matsen closed 13 years ago
1
merge alpha11 into master

#174 matsen closed 12 years ago
0
Hi! I cleaned up your code for you!

#173 GunioRobot closed 13 years ago
0
xml-light is broken; switch to using xmlm

#172 habnabit closed 13 years ago
0
make summary information available from convexify

#171 matsen closed 12 years ago
1
make sure FastTree placement with protein sequences working

#170 matsen closed 13 years ago
2
all commands that take reference packages should use -c flag

#169 matsen closed 13 years ago
0
have (guppy|rppr) --help also spit out the list of subcommands

#168 matsen closed 13 years ago
1
lacking bark?

#167 matsen closed 13 years ago
1
Not_found error in guppy sing, tog

#166 cmccoy closed 13 years ago
2
de-clobbering site categories

#165 matsen closed 13 years ago
1
internal node labels make ref_tree choke (and perhaps some other things too?)

#164 matsen closed 13 years ago
0
make a --numbered option for outputting a tree with numbers on the edge

#163 matsen closed 13 years ago
0
more sophisticated way of doing initial ranking

#162 matsen closed 13 years ago
3
add a --pre-round to guppy squash

#161 matsen closed 13 years ago
0
rppr info assumes a taxonomy is part of the reference package

#160 matsen closed 13 years ago
1
update to batteries v2

#159 habnabit closed 13 years ago
0
have the informative branch length prior depend on edge position

#158 matsen opened 13 years ago
0
`compress` command to combine pqueries that are within a certain distance

#157 matsen closed 13 years ago
2
computing lots of KR distances at once

#156 matsen closed 13 years ago
1
move the functionality of pplacer --pretend to pre-masking

#155 habnabit closed 13 years ago
1
infer islands of mass

#154 matsen closed 13 years ago
1
mft shouldn't transform into mass automatically (I think)

#153 matsen closed 13 years ago
1
try an early termination for voronoi full

#152 matsen closed 12 years ago
1
make a voronoi leaf adding functionality

#151 matsen closed 11 years ago
2
logging for voronoi

#150 matsen closed 13 years ago
0
branch labels and node labels should be saved

#149 matsen closed 13 years ago
5
test out default values of parameters

#148 matsen opened 13 years ago
0
make a one-parameter family of functions generalizing wpd

#147 matsen closed 13 years ago
0
unweighted edge PCA

#146 matsen closed 12 years ago
3
merge alpha10 into master

#145 matsen closed 13 years ago
1
improve handling of unplaced sequences

#144 matsen closed 13 years ago
1
specify number of sequences to keep in voronoi

#143 matsen closed 13 years ago
0
make full recursion for voronoi

#142 matsen closed 13 years ago
0
add some sort of documentation for scripts

#141 matsen closed 13 years ago
0
pplacer does not recognize reference sequences in alignment

#140 cmccoy closed 13 years ago
1
pplacer should warn if there is an all-gap reference after pre-masking

#139 matsen closed 13 years ago
1
tear transform out of everywhere and then put it in mft

#138 matsen closed 13 years ago
1
add a flag to convexify to print the number of questions asked

#137 matsen closed 13 years ago
2
remove `transform` from Mass_map; make `weighting` optional

#136 habnabit closed 13 years ago
1
more robust error messages

#135 matsen closed 13 years ago
3
implement a generalized way of specifying output formats for tabular data

#134 matsen closed 13 years ago
0

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