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@yangfangs yangfangs released this Dec 5, 2019 · 3 commits to master since this release

Update

  • Update the PhySpeTree cite information.

Bugs fix

  • Fix RAxML can't run with multi-thread problem
Assets 2

@yangfangs yangfangs released this Oct 3, 2019 · 6 commits to master since this release

Update

  • Update RAxML version: v8.2.3 --> v8.2.12.
  • Update mafft version: v7.407-->v7.429.
  • Update third-party software cites.
  • Add SPRSupertree software to combine module (--supertree option) for combining conflicting evolutionary histories that are due to lateral gene transfer (LGT).
Assets 2

@yangfangs yangfangs released this Sep 21, 2019 · 13 commits to master since this release

Update

  • Add ''-db" option for build species tree by the local database (can't connect to the Internet).
  • Add ASTRAL software to combine module (--astral option) for merging more gene trees.

Bugs fix

  • Fix retrieve hcp proteins more than 500 species bug.
  • Fix concatenate HCP database time out question.
Assets 2

@yangfangs yangfangs released this Jun 3, 2019 · 37 commits to master since this release

Update

  • Updated supported kegg database version (Release 88.2 ----> 90.1) and the HCP method supported 5943 organisms (old version: 5662).
Assets 2

@yangfangs yangfangs released this Jan 10, 2019 · 40 commits to master since this release

Update

  • Update the the pipeline contains mafft softwere to v7.407 (old: v7.310).

New feature

  • Add new reconstruct phylogenetic tree (IQ-TREE v1.6.9) software to pipeline
Assets 2

@yangfangs yangfangs released this Aug 2, 2018 · 43 commits to master since this release

Update

  • Released a new version of PhySpeTree that supports both Python2+ and Python3+.

  • The organisms supported by the HCP method was updated by the KEGG database (version 88.2, November 1, 2018) and HCP method support 5662 species.

  • The organisms supported by the SURNA pre-build databse was updated by SILVA database (Release 132, Released: 13.12.2017) and SURNA method support 140662 species.

New feature

  • Now PhySpeTree not only supported the user input three- or four-letter organism codes (KEGG database organism codes) but also the NCBI taxonomy id (for example human taxonomy id is 9606).
Assets 2

@yangfangs yangfangs released this Jun 22, 2018 · 49 commits to master since this release

Fix str bug

  • Fix the input str sometime can't read.
Assets 2

@yangfangs yangfangs released this Nov 18, 2018 · 52 commits to master since this release

Update

  • Updated KEGG_DB
Assets 2

@yangfangs yangfangs released this Mar 7, 2018 · 55 commits to master since this release

Update

  • Update build model parameter "--hcp" to "--multiple" .
  • Update build model parameter "--sran" to "--single".
  • Update online manual.
Assets 2

@yangfangs yangfangs released this Jan 13, 2018 · 59 commits to master since this release

Update

  • update the kegg db index

Bugs fix

  • fix the default '--hcp' method as default useless
Assets 2
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