PhySpeTree 0.3.9

Update

• Update the PhySpeTree cite information.

Bugs fix

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

PhySpeTree 0.3.8

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).

PhySpeTree 0.3.7

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.

PhySpeTree 0.3.6

Update

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

PhySpeTree 0.3.5

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

PhySpeTree 0.3.4

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).

PhySpeTree 0.3.3

Fix str bug

• Fix the input str sometime can't read.

PhySpeTree 0.3.2

Update

• Updated KEGG_DB

PhySpeTree 0.3.1

Update

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

PhySpeTree 0.3.0

Update

• update the kegg db index

Bugs fix

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