Imperial College London
Alternate

Dr Kambiz N. Alavian, PhD, SFHEA, FLS, FRSB

Faculty of Medicine, Department of Brain Sciences

Reader in Neuroscience
 
 
 
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Contact

 

+44 (0)20 7594 7006k.alavian Website

 
 
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Assistant

 

Mrs Hadeel Abdeen +44 (0)20 7594 7014

 
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Location

 

E507Burlington DanesHammersmith Campus

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Summary

 

Publications

Citation

BibTex format

@article{Fang:2019:10.1186/s12862-019-1541-x,
author = {Fang, Y and Liu, C and Lin, J and Li, X and Alavian, KN and Yang, Y and Niu, Y},
doi = {10.1186/s12862-019-1541-x},
journal = {BMC Evolutionary Biology},
pages = {1--8},
title = {PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees},
url = {http://dx.doi.org/10.1186/s12862-019-1541-x},
volume = {19},
year = {2019}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - BackgroundPhylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediate steps, such as processing extremely large sequences and preparing configure files to connect multiple software. When the species number is large, the intermediate steps become a bottleneck that may seriously affect the efficiency of tree building.ResultsHere, we present an easy-to-use pipeline named PhySpeTree to facilitate the reconstruction of species trees across bacterial, archaeal, and eukaryotic organisms. Users need only to input the abbreviations of species names; PhySpeTree prepares complex configure files for different software, then automatically downloads genomic data, cleans sequences, and builds trees. PhySpeTree allows users to perform critical steps such as sequence alignment and tree construction by adjusting advanced options. PhySpeTree provides two parallel pipelines based on concatenated highly conserved proteins and small subunit ribosomal RNA sequences, respectively. Accessory modules, such as those for inserting new species, generating visualization configurations, and combining trees, are distributed along with PhySpeTree.ConclusionsTogether with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). The source code is freely available with detailed documentation (https://github.com/yangfangs/physpetools).
AU  - Fang,Y
AU  - Liu,C
AU  - Lin,J
AU  - Li,X
AU  - Alavian,KN
AU  - Yang,Y
AU  - Niu,Y
DO  - 10.1186/s12862-019-1541-x
EP  - 8
PY  - 2019///
SN  - 1471-2148
SP  - 1
TI  - PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees
T2  - BMC Evolutionary Biology
UR  - http://dx.doi.org/10.1186/s12862-019-1541-x
UR  - https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-019-1541-x
UR  - http://hdl.handle.net/10044/1/75594
VL  - 19
ER  -
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