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lmaurits
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phyltr
Unix filters for manipulating and analysing (samples of) phylogenetic trees represented in the Newick format
GNU General Public License v3.0
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Something is physhy in the consensus trees
#37
Anaphory
opened
3 years ago
6
Current sink absorbs internal node names
#36
Anaphory
opened
4 years ago
1
Add two commands
#35
Anaphory
opened
4 years ago
3
Newick Networks
#34
Anaphory
opened
5 years ago
1
Command line usage results in "unrecognized arguments", followed by the .nex file
#33
fmatter
opened
5 years ago
2
Fixes import error
#32
tresoldi
closed
5 years ago
2
pep8 + refactoring mean/median/HPD computation
#31
xrotwang
closed
5 years ago
2
should phyltr be pluggable?
#30
xrotwang
opened
5 years ago
1
`clades` command should output a CSV file, for overall consistency
#29
lmaurits
opened
5 years ago
0
Remove omnipresent files argument
#28
xrotwang
closed
5 years ago
5
first stab at phyltr 1.0
#27
xrotwang
closed
5 years ago
4
phyltr.main._COMMANDS lists non-existing commands
#26
xrotwang
opened
5 years ago
0
Inconsistent CLI syntax for taxa
#25
xrotwang
closed
5 years ago
13
Another reason to drop py2 support: statistics!
#24
xrotwang
closed
5 years ago
1
Rename main.py to __main__.py
#23
xrotwang
closed
5 years ago
0
Replace optparse with argparse
#22
xrotwang
opened
5 years ago
0
More flexible rename map
#21
xrotwang
opened
5 years ago
11
phyltr cat does not read NEXUS translate block correctly
#20
xrotwang
closed
5 years ago
6
Consensus tree calculation pretends to run on mixed trees
#19
Anaphory
opened
5 years ago
5
specify release process
#18
xrotwang
opened
5 years ago
1
Refactored classmethods, more tests and better custom Nexus support
#17
xrotwang
closed
5 years ago
3
unsupported nexus format
#16
xrotwang
closed
5 years ago
8
refactored test suite, using pytest fixtures to remove boilerplate
#15
xrotwang
closed
5 years ago
1
Fix clades command for edge case of single taxon tree
#14
xrotwang
closed
5 years ago
1
IndexError in save_clade_report
#13
xrotwang
closed
5 years ago
2
Phyltr-generated treestreams are not guaranteed to have a fixed taxon set, but some commands assume they will
#12
lmaurits
opened
5 years ago
0
all tests pass on py3.5
#11
xrotwang
closed
5 years ago
9
port to py3
#10
xrotwang
opened
5 years ago
1
Cat seems to not work in chunks
#9
Anaphory
closed
6 years ago
1
Somewhere in phyltr, all tips are aligned
#8
Anaphory
opened
6 years ago
6
Import of main should be relative
#7
Anaphory
closed
6 years ago
1
Implement --no-annotations
#6
Anaphory
closed
6 years ago
6
See if funky argument handling can be made more elegant
#5
lmaurits
opened
7 years ago
0
Implement siblings command
#4
lmaurits
closed
7 years ago
0
Implement grep command
#3
lmaurits
closed
7 years ago
0
Support summarising discrete annotations (e.g. ancestral state reconstructions)
#2
lmaurits
opened
7 years ago
0
Trees with BEAST/FigTree-ish annotations fail to parse
#1
tgvaughan
opened
9 years ago
4