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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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Documentation out of sync with code?
#121
nylander
closed
1 year ago
3
Handling circular taxonomic lineages
#120
crosenth
closed
4 years ago
1
Entered LG-model (Fasttree) in lines 116 and 150
#119
sachacoesel
closed
6 years ago
1
update to python 3.6 in docker image
#118
nhoffman
closed
5 years ago
2
produce table of lineages represented as taxonomic names
#117
nhoffman
closed
6 years ago
1
taxtastic cohort error
#116
ghost
closed
6 years ago
13
enforcing python2
#115
crosenth
closed
5 years ago
0
adding psycopg2 to install requirements
#114
dhoogest
closed
6 years ago
2
Fixed column order and added check for self-reference to root
#113
jgolob
closed
7 years ago
1
column order and need for self-referrential root
#112
jgolob
opened
7 years ago
0
adding schema prefix to queries for postgres compatibility
#111
dhoogest
closed
7 years ago
0
Consider using ncbi taxcat to process species clades
#110
crosenth
closed
6 years ago
0
remove dependency on biopython
#109
nhoffman
closed
6 years ago
0
remove dependency on pandas
#108
nhoffman
closed
6 years ago
2
develop.rst merge from 3 years ago
#107
crosenth
closed
7 years ago
0
taxtastic - new versions - in BioConda?
#106
AjitPS
closed
6 years ago
2
Regular build of a full ncbi taxtable
#105
crosenth
closed
6 years ago
3
taxtable column order must be tax_id, parent_id, rank, tax_name, ranks
#104
nhoffman
closed
7 years ago
1
create docker image
#103
nhoffman
closed
7 years ago
0
Unfiltered taxonomy
#102
dhoogest
closed
7 years ago
1
add_node(s) refactor
#101
crosenth
closed
7 years ago
0
use recursive cte to calculate lineages
#100
nhoffman
closed
6 years ago
1
evaluate leaving no_rank taxa in database and expanding on the fly
#99
nhoffman
closed
6 years ago
2
postgresql database creation
#98
nhoffman
opened
7 years ago
0
add_ranks subcommand
#97
crosenth
closed
6 years ago
2
add_names subcommand
#96
crosenth
closed
6 years ago
2
Update Sphinx docs on latest tagged version
#95
crosenth
closed
6 years ago
1
commented out regex for excluding 'group' records
#94
dhoogest
closed
7 years ago
4
Remove "group" from UNCLASSIFIED_REGEX_COMPONENTS in ncbi.py
#93
dhoogest
closed
7 years ago
2
"source" table not updated with add_nodes
#92
nhoffman
opened
7 years ago
1
Populate source table when adding initial data in subcommand ``new_database``
#91
crosenth
closed
7 years ago
1
PyPI package out of date?
#90
wwood
closed
7 years ago
3
Is it possible to run pplacer on an IQ-tree?
#89
AliciaArroyo
closed
3 months ago
2
running taxit error. pkg_resources.DistributionNotFound: xlrd
#88
blancaverag
closed
6 years ago
3
Fast taxtable
#87
crosenth
closed
7 years ago
2
Add ordered table "ranks" to `taxit new_database` construction
#86
crosenth
closed
7 years ago
1
move --append-lineage to separate subcommand for use after taxit add_nodes
#85
crosenth
closed
7 years ago
0
``taxit update_taxids`` ``--ignore-unknowns`` and ``--taxid-column``
#84
crosenth
closed
8 years ago
1
Migrate to python3
#83
crosenth
closed
6 years ago
4
new function taxtable.remove_subtree()
#82
crosenth
closed
8 years ago
0
taxtable.subtree_sequence_ids does not return all sequence_ids in subtree
#81
crosenth
closed
8 years ago
1
Feature request: taxtable.remove_subtree(tax_id)
#80
crosenth
closed
8 years ago
1
use local copy of ncbi taxdump
#79
kbseah
closed
7 years ago
2
use pandas.read_sql_table for update_taxids and is_classified
#78
crosenth
closed
7 years ago
1
subcommand to merge two or more tax tables
#77
nhoffman
closed
8 years ago
1
Count taxids
#76
crosenth
closed
8 years ago
0
count tax_id appearances in a taxtable lineage
#75
crosenth
closed
8 years ago
1
adding new names
#74
aubreymoore
closed
6 years ago
2
Would like a function that given a tax_id and rank returns the tax_id at that rank in the lineage
#73
crosenth
closed
8 years ago
1
Taxid classified
#72
crosenth
closed
8 years ago
0
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