PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees

PhySpeTree is implemented in Python language (supports Python2.7+ and Python3+), designed for Linux systems (docker for Windows OS or Mac OS).


Understanding phylogenetic relationships between different species is crucial for evolutionary studies. Reconstructing the phylogenetic species tree, a branching diagram, is particularly useful in inferring evolutionary relationships. For example, the tree-of-life provides a remarkable view of organizing principles of the biological world. In addition, because new organisms are being sequenced, by integrating them to already built species trees, it is important to determine their taxonomic identities. Moreover, combining with gain/loss homologous information, species trees are widely applied in predicting new members of protein complexes and protein-protein interactions.

Here, we developed an easy-to-use package named PhySpeTree that is convenient to reconstruct species trees by one command line. Two independent pipelines were included by using the most adopted small subunit ribosomal RNA (SSU rRNA) and concatenated highly conserved proteins (HCP), respectively. A distinct advantage is that users only need to input species names and PhySpeTree automatically downloads and analyzes sequences of SSU rRNA about 140,662 species and HCP about 5,900 organisms.





PhySpeTree autobuild -i species_name_list.txt --hcp
PhySpeTree build -i species.fasta -o --multiple
PhySpeTree combine -i multiple_tree.tree -o Output
PhySpeTree iview -i species_name_list.txt -o ivew -range phylum 
PhySpeTree check -i organisms.txt -o checkout --protein

Cite: Fang, Y., Liu, C., Lin, J. et al. PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees. BMC Evol Biol 19, 219 (2019) doi:10.1186/s12862-019-1541-x