Issues

• Build new 2018 UNITE ghost trees

  JTFouquier/ghost-tree#95 · Filter by author JTFouquier opened on Mar 13, 2019

• Update Python version for ghost-tree compatibility with QIIME 2 2019.1 release

  bughigh priority
  JTFouquier/ghost-tree#94 · Filter by author JTFouquier opened on Feb 18, 2019
  2

• Update readme to include pictures; refs to QIIME 2 analysis steps

  JTFouquier/ghost-tree#90 · Filter by author JTFouquier opened on Aug 16, 2018

• ghost-tree tip file name needs to be consistent

  quick fix
  JTFouquier/ghost-tree#89 · Filter by author JTFouquier opened on Jun 6, 2018

• Analysis: Determine effects of clustering at different levels

  enhancement
  JTFouquier/ghost-tree#88 · Filter by author JTFouquier opened on May 10, 2018

• Update ghost-tree docs (including removing docs for use in QIIME 1)

  documentation
  JTFouquier/ghost-tree#87 · Filter by author JTFouquier opened on May 10, 2018

• Extract fungi from Silva database is 'genus' specific; Fix this for other ranks

  high priority
  JTFouquier/ghost-tree#86 · Filter by author JTFouquier opened on May 7, 2018

• Select the longest sequence within each genus

  enhancement
  JTFouquier/ghost-tree#85 · Filter by author vmikk opened on Apr 24, 2018
  1

• Allow option to print ascii art

  nice to have
  JTFouquier/ghost-tree#84 · Filter by author JTFouquier opened on Apr 23, 2018

• Remove dependency on OTU picking

  high priority
  JTFouquier/ghost-tree#82 · Filter by author JTFouquier opened on Mar 15, 2018
  2

• Improve taxonomy line issues in files (i.e. allow taxonomy to be in different locations)

  enhancement
  JTFouquier/ghost-tree#79 · Filter by author JTFouquier opened on Jan 31, 2017
  1

• write script to automate tree building

  enhancement
  JTFouquier/ghost-tree#78 · Filter by author JTFouquier opened on Dec 12, 2016

• Consider adding user suggestions and provided scripts by author "R.A."

  enhancement
  JTFouquier/ghost-tree#74 · Filter by author JTFouquier opened on Sep 30, 2016

• make get_otus_from_ghost_tree.py more elegant (users shouldn't have to edit the script...)

  quick fix
  JTFouquier/ghost-tree#68 · Filter by author JTFouquier opened on Mar 30, 2016

• Build trees with new Silva (foundation tree) release

  JTFouquier/ghost-tree#64 · Filter by author JTFouquier opened on Feb 16, 2016

• Add same filter step for extensions as foundation tree

  high priority
  JTFouquier/ghost-tree#59 · Filter by author JTFouquier opened on Dec 6, 2015

• Add option for user to scale branch lengths

  high priority
  JTFouquier/ghost-tree#57 · Filter by author JTFouquier opened on Dec 1, 2015
  4

• Allow option for Generalized Time Reversible (GTR) model to be selected instead of Jukes Cantor

  enhancement
  JTFouquier/ghost-tree#55 · Filter by author JTFouquier opened on Nov 7, 2015

• Try adding a Click progress bar (for large files ghost-tree takes some time)

  nice to have
  JTFouquier/ghost-tree#51 · Filter by author JTFouquier opened on Aug 15, 2015
  1

• add ascii_art demo using skbio to ghost-tree tutorial

  nice to have
  JTFouquier/ghost-tree#50 · Filter by author JTFouquier opened on Aug 15, 2015

• ghost-tree output files are in a folder now; provide alternative option to name files

  enhancement
  JTFouquier/ghost-tree#49 · Filter by author JTFouquier opened on Jul 23, 2015
  6

• analyze the effect of grafting trees in the wrong place

  JTFouquier/ghost-tree#40 · Filter by author gregcaporaso opened on May 6, 2015 · AfterSubmission

• explore scaling of extension tree branch lengths relative to foundation tree

  question
  JTFouquier/ghost-tree#39 · Filter by author gregcaporaso opened on May 6, 2015 · BeforeSubmission

• Add warning into the docs about potential for clustered sequences to be mislabeled

  documentationhigh priority
  JTFouquier/ghost-tree#36 · Filter by author wasade opened on May 6, 2015 · AfterSubmission

• Improve code complexity in ghosttree.scaffold

  invalid
  JTFouquier/ghost-tree#33 · Filter by author JTFouquier opened on May 6, 2015 · AfterSubmission
  1