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- 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).
- 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.
- Fix retrieve hcp proteins more than 500 species bug.
- Fix concatenate HCP database time out question.
- Update the the pipeline contains mafft softwere to v7.407 (old: v7.310).
- Add new reconstruct phylogenetic tree (IQ-TREE v1.6.9) software to pipeline
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.
- 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).