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fhcrc
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taxtastic
Create and maintain phylogenetic "reference packages" of biological sequences.
GNU General Public License v3.0
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drop support for excel imputs
#71
nhoffman
closed
8 years ago
1
generate docs using CLI help text
#70
nhoffman
closed
8 years ago
1
update_taxids requires seq_info when just list of taxids would suffice
#69
tyleraland
closed
8 years ago
2
query ncbi entrez for accession tax_ids
#68
crosenth
closed
8 years ago
2
UnicodeDecodeError
#67
GuangchuangYu
closed
9 years ago
5
Suppress warning on `taxit update` of `tree_stats`
#66
cmccoy
closed
10 years ago
0
Error initializing submodule html
#65
crosenth
closed
10 years ago
3
Empirical frequencies for phyml?
#64
matsen
closed
10 years ago
1
FastTree AA models should have `empirical_frequencies: false`
#63
cmccoy
closed
10 years ago
0
Doesn't make an "empirical_frequencies" key when doing AA for phyml
#62
matsen
closed
10 years ago
0
Latest PhyML stats files fail parsing
#61
cmccoy
closed
11 years ago
0
Subcommand to add nodes to taxtable
#60
cmccoy
closed
11 years ago
0
is_classified should operate on species name only instead of each tax_name
#59
nhoffman
closed
11 years ago
0
taxtastic-0.4.0 installation error
#58
koadman
closed
11 years ago
1
taxonomic rerooting by default for new refpkgs
#57
cmccoy
closed
12 years ago
0
Subcommand to update tax_ids
#56
cmccoy
closed
12 years ago
0
Support running `taxit taxtable` with a sequence info file
#55
cmccoy
closed
12 years ago
0
Support PhyML stats files in `taxit create`
#54
cmccoy
closed
12 years ago
0
integrate rppr infer into taxit
#53
matsen
closed
10 years ago
0
confirm and test that version number with git sha makes it into refpkg metadata
#52
nhoffman
closed
10 years ago
0
`util.parse_fasttree` fails to parse WAG model
#51
cmccoy
closed
12 years ago
0
add `rp` command to taxit for inspecting refpkg contents
#50
habnabit
closed
12 years ago
0
Stats file parsing fails for RAxML 7.2.5
#49
cmccoy
closed
12 years ago
0
check CONTENTS.json tree_file and phylo_model_file tags in v0.3.1
#48
benjsmith
closed
12 years ago
1
issue in docs on ghpages should follow taxtastic.__init.__.__version.__
#47
nhoffman
closed
10 years ago
1
seq_info required fields
#46
nhoffman
closed
12 years ago
0
Update readme
#45
madhadron
closed
10 years ago
0
Make common fields in refsets be named in a human readable manner
#44
madhadron
closed
12 years ago
1
Dependency on decorator missing
#43
cmccoy
closed
13 years ago
0
pretty-print CONTENTS.json
#42
nhoffman
closed
13 years ago
0
don't include rollback information on initial package creation
#41
nhoffman
closed
13 years ago
2
make `taxit reroot` really call `rppr reroot`
#40
habnabit
closed
13 years ago
0
prepare ref pkgs from FastTree trees
#39
matsen
closed
12 years ago
4
taxtable -d required?
#38
smirarab
closed
13 years ago
3
add `taxit update` for updating a refpkg's contents
#37
habnabit
closed
13 years ago
0
clean up scripts in top level
#36
nhoffman
closed
13 years ago
3
look into incorporating greengenes taxonomy into taxtastic
#35
nhoffman
closed
1 year ago
2
make keys in CONTENTS.json more consistent
#34
nhoffman
closed
13 years ago
1
Make get_lineage automatically call _get_merged (with option to disable it)
#33
madhadron
closed
13 years ago
0
Remove readme extraction from ncbi fetching functions
#32
madhadron
closed
13 years ago
0
Need unit test to test failure of clobber in create command
#31
madhadron
closed
13 years ago
0
tighten up relationship between package version and git tag
#30
nhoffman
closed
13 years ago
1
implement `taxit check_refpkg`
#29
nhoffman
closed
13 years ago
0
more robust taxonomic rerooting
#28
matsen
closed
13 years ago
1
taxit reroot errors when TMPDIR is a different file system
#27
cmccoy
closed
13 years ago
0
tog appends multiple taxa together with a _ when sequences are identical
#26
smirarab
closed
13 years ago
2
taxit reroot deletes current reference tree on write error
#25
cmccoy
closed
13 years ago
0
need some sort of more flexible gene identifier
#24
matsen
closed
13 years ago
0
reroot should warn if taxonomic rooting is not unique
#23
matsen
closed
13 years ago
2
taxit allows creation of empty reference packages
#22
matsen
closed
13 years ago
1
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