JTFouquier ghost-tree issues

JTFouquier / ghost-tree

creating hybrid-gene phylogenetic trees for diversity analyses

BSD 3-Clause "New" or "Revised" License

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issues

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Build new 2018 UNITE ghost trees

#95 JTFouquier opened 5 years ago
0
Update Python version for ghost-tree compatibility with QIIME 2 2019.1 release

#94 JTFouquier opened 5 years ago
2
Test issue for a git demo

#93 JTFouquier closed 5 years ago
0
Prevent skbio from causing import QtCore via matplotlib

#92 epruesse closed 6 years ago
1
merge travis error fixes into master

#91 JTFouquier closed 6 years ago
0
Update readme to include pictures; refs to QIIME 2 analysis steps

#90 JTFouquier opened 6 years ago
0
ghost-tree tip file name needs to be consistent

#89 JTFouquier opened 6 years ago
0
Analysis: Determine effects of clustering at different levels

#88 JTFouquier opened 6 years ago
0
Update ghost-tree docs (including removing docs for use in QIIME 1)

#87 JTFouquier opened 6 years ago
0
Extract fungi from Silva database is 'genus' specific; Fix this for other ranks

#86 JTFouquier opened 6 years ago
0
Select the longest sequence within each genus

#85 vmikk opened 6 years ago
1
Allow option to print ascii art

#84 JTFouquier opened 6 years ago
0
Use correct tempfile library in Python

#83 JTFouquier closed 6 years ago
0
Remove dependency on OTU picking

#82 JTFouquier opened 6 years ago
2
error in build ghost-tree at last step

#81 NElight closed 6 years ago
4
skbio.io._exception.IOSourceError when i build the tree

#80 NElight closed 7 years ago
7
Improve taxonomy line issues in files (i.e. allow taxonomy to be in different locations)

#79 JTFouquier opened 7 years ago
1
write script to automate tree building

#78 JTFouquier opened 7 years ago
0
ghost-tree update to skbio 5.0? Yes or no?

#77 JTFouquier closed 7 years ago
11
possible issue with newer versions of FastTree (2.1.8 & 2.1.9)

#76 JTFouquier closed 7 years ago
2
Error while updating to the new SILVA and UNITE releases

#75 vmikk closed 7 years ago
8
Consider adding user suggestions and provided scripts by author "R.A."

#74 JTFouquier opened 7 years ago
0
ghost-tree update to Python 3.4 for QIIME 2 plugin

#73 JTFouquier closed 7 years ago
1
beta_diversity_through_plots

#72 aves920 closed 7 years ago
9
add parentheses to print

#71 vmikk closed 8 years ago
2
add parentheses to print

#70 vmikk closed 8 years ago
0
Phylogenetic placement on a ghost-tree

#69 vmikk closed 7 years ago
7
make get_otus_from_ghost_tree.py more elegant (users shouldn't have to edit the script...)

#68 JTFouquier opened 8 years ago
0
Underscore compatibility

#67 fanli-gcb closed 8 years ago
3
Update README.rst

#66 jamespharper closed 8 years ago
4
Build and upload trees based on code modification for manuscript/publication

#65 JTFouquier closed 8 years ago
1
Build trees with new Silva (foundation tree) release

#64 JTFouquier opened 8 years ago
0
change wording to include foundation, not scaffold to be consistent with manuscript

#63 JTFouquier closed 8 years ago
1
Fix subprocess.communicate for FastTree installation (var issue)

#62 JTFouquier closed 8 years ago
0
Build new trees for new UNITE DBs & updated ghost-tree code

#61 JTFouquier closed 8 years ago
1
ghost-tree is "genus" specific, there are cases (e.g., LSU needs order) needing higher levels

#60 JTFouquier closed 6 years ago
1
Add same filter step for extensions as foundation tree

#59 JTFouquier opened 8 years ago
0
root foundation tree by midpoint

#58 JTFouquier closed 8 years ago
0
Add option for user to scale branch lengths

#57 JTFouquier opened 8 years ago
4
Update "get_otus... " to maintain underscores (not default in skbio)

#56 JTFouquier closed 8 years ago
0
Allow option for Generalized Time Reversible (GTR) model to be selected instead of Jukes Cantor

#55 JTFouquier opened 8 years ago
0
keep current check for "g__" but if some lines don't contain it, then assume g__unidentified

#54 JTFouquier closed 6 years ago
1
Add/organize files for revision of ghost-tree paper

#53 JTFouquier closed 7 years ago
0
CI: use flake8 default include/exclude patterns; include all scripts explicitly

#52 jairideout closed 9 years ago
0
Try adding a Click progress bar (for large files ghost-tree takes some time)

#51 JTFouquier opened 9 years ago
1
add ascii_art demo using skbio to ghost-tree tutorial

#50 JTFouquier opened 9 years ago
0
ghost-tree output files are in a folder now; provide alternative option to name files

#49 JTFouquier opened 9 years ago
6
Output tips only for filter_otus_from_otu_table.py in QIIME

#48 JTFouquier closed 9 years ago
1
fix SUMACLUST link

#47 JTFouquier closed 9 years ago
0
improved documentation of which reference fasta files to use for which ghost-trees

#46 gregcaporaso closed 9 years ago
2