SpeciesTree: an easy-to-use and robust pipeline for eukaryotic species tree construction

Table of contents

• Introduction

• Features

• Dependencies

• Installation

• Running

• Contact

Introduction

SpeciesTree is a useful tool to construct species trees using stringent single-copy nuclear genes across multiple species. It has been demonstrated to be useful in both plants and animals. SpeciesTree is totally free and open source to the public. 

Features

1. Easy-to-use. The procedures and requirements is listed below. Compared to other available tools, SpeciesTree is rather easy and useful for both animal scientists and plant biologists.
2. Robust. We have tested SpeciesTree using both data from animals and plants. SpeciesTree is useful for small number of species and for more than one hundred species.
3. The process of tree construction is highly automated. Users just need to input the CDS and protein files from multiple species, and the output files were: a table of single-copy nulear genes, two tree files in newick format (one based on coalescent method, the other one based on supermatrix method), two PDF and two png files of species trees.

Dependencies

Following are a list of third-party programs that will be used in SpeciesTree pipeline. These dependencies are required to be installed and added in your PATH before running this script.

• OrthoFinder v2.0.0+
• MCL
• BLAST+
• Diamond
• MAFFT
• MUSCLE
• trimAl
• RAxML
• Python2.7+
• ggtree

Installation

1. Download and install the dependencies

   # OrthoFinder installing
   $ wget https://github.com/davidemms/OrthoFinder/releases/download/v2.2.7/OrthoFinder-2.2.7.tar.gz
   $ tar xzvf OrthoFinder-2.2.7.tar.gz
   $ export PATH=$PATH:/your/path/to/orthofinder
   
   # MCL installing
   $ sudo apt-get install mcl
   
   # BLAST+ installing
   $ sudo apt-get install ncbi-blast+
   
   # Diamond installing
   $ wget https://github.com/bbuchfink/diamond/releases/download/v0.9.22/diamond-linux64.tar.gz
   $ tar xzf diamond-linux64.tar.gz
   $ export PATH=$PATH:/your/path/to/diamond
   
   # MAFFT installing
   $ wget https://mafft.cbrc.jp/alignment/software/mafft-7.407-without-extensions-src.tgz
   $ tar xzvf mafft-7.407-without-extensions-src.tgz
   $ cd mafft-7.407-without-extensions-src/core/
   $ make
   $ export PATH=$PATH:/your/path/to/mafft
   
   # MUSCLE installing
   $ wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
   $ tar xzvf muscle3.8.31_i86linux64.tar.gz
   $ mv muscle3.8.31_i86linux64 muscle
   $ export PATH=$PATH:/your/path/to/muscle
   
   # trimAl installing
   $ wget https://github.com/scapella/trimal/archive/trimAl.zip
   $ unzip trimAl.zip && cd trimal-trimAl/source/
   $ make
   $ export PATH=$PATH:/your/path/to/trimal
   
   # RAxML installing
   $ wget https://github.com/stamatak/standard-RAxML/archive/master.zip
   $ unzip master.zip && cd standard-RAxML-master/
   $ make -f Makefile.PTHREADS.gcc && rm *.o
   $ export PATH=$PATH:/your/path/to/raxmlHPC-PTHREADS
   
   # ggtree installing
   # To install this package, start R (version "3.5") and enter:
   $ if (!requireNamespace("BiocManager", quietly = TRUE))
   $ 	install.packages("BiocManager")
   $ BiocManager::install("ggtree", version = "3.8")

2. Download and install the SpeciesTree

   $ cd ~/biosoft/ # or any directory of your choice
   $ git clone https://github.com/Davey1220/SpeciesTree.git
   $ cd SpeciesTree/
   # Setup the SpeciesTree 
   # Check dependencies and configure SpeciesTree
   $ bash setup.sh 
   $ ~/biosoft/SpeciesTree/SpeciesTree.sh -h
   Usage:
   SpeciesTree.sh -p pep_file_dir -n cds_file_dir 
   [-S search_Program (diamond)] [-A msa_Program (mafft)]
   [-t num_Threads (16)] [-b num_Bootstraps (100)] 
   [-m aa_SubstitutionModel (PROTGAMMAJTT)] 
   [-M nucl_SubstitutionModel (GTRGAMMA)]
   [-o outGroupName1[,outGroupName2[,...]]] [-h]
   ----------------------------------------------------------------------------------------------
   Filename:    SpeciesTree.sh
   Revision:    v1.0
   Date:        2018/10/24
   Author:      Wei Dong
   Email:       1369852697@qq.com
   GitHub:      https://github.com/Davey1220/
   Description: This script was designed to construct species tree 
   ----------------------------------------------------------------------------------------------
   Version v1.0 2018/10/24
   
   Options:
       -p: Offer protein files with the fasta format in pep_file_dir. (required)
       -n: Offer cds files with the fasta format in cds_file_dir. (required)
       -S: Use search_program for alignment search. [Options: diamond, blast, default is diamond]
       -A: Perform multiple sequences alignment. [Options: mafft, muscle, default is mafft]
       -t: Set the number of threads. [Default is 16]
       -b: Perform multiple bootstrap analysis. [Default is 100]
       -m: Set the model of amino acid substitution. [Default is PROTGAMMAJTT]
       -M: Set the model of nucleotide substitution. [Default is GTRGAMMA]
       -o: Specify the name of a single outgroup or a comma-separated list of outgroups, eg "-o Rat" or "-o Rat,Mouse".
       -h/?: Show this help message and exit.
   
   Example:
       SpeciesTree.sh -p test_pep/ -n test_cds/ -S diamond -A mafft -t 20 -b 100 -m PROTGAMMAJTT -M GTRGAMMA -o speciesA

Running

$ curl -O http://112.74.50.115/Example.tar.gz

$ tar xzvf Example.tar.gz

$ ~/biosoft/SpeciesTree/SpeciesTree.sh -p Example/pep/ -n Example/cds/ -S diamond -A mafft -t 20 -b 100 -M PROTGAMMAJTT -m GTRGAMMA

Homepage

http://www.eplant.org/speciestree.html

Contact

Mr. Wei Dong, 1369852697@qq.com

Dr. Fei Chen, bioinforchen@163.com