• Users could down the SpeciesTree tool here.


    1. System requirement

    MAC OS; Linux OS

    1.1 Download and install the dependencies

                            # OrthoFinder installing
    $ wget
    $ 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
    $ 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-
    $ 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
    $ 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-
    $ 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")

    1.2 Download and install the SpeciesTree

                            $ cd ~/biosoft/ # or any directory of your choice
    $ curl -O http://chibba.pgml.uga.edu/snphylo/snphylo.tar.gz
    $ tar xvfz snphylo.tar.gz
    $ cd SpeciesTree/
    # Setup the SpeciesTree
    # Check dependencies and configure SpeciesTree
    $ bash setup.sh
    $ ~/biosoft/SpeciesTree/SpeciesTree.sh -h
    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
    -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.
    -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
    -M: Set the model of nucleotide substitution. [Default is
    -o: Specify the name of a single outgroup or a commaseparated
    list of outgroups, eg "-o Rat" or "-o Rat,Mouse".
    -h/?: Show this help message and exit.
    SpeciesTree.sh -p test_pep/ -n test_cds/ -S diamond -A mafft
    -t 20 -b 100 -m PROTGAMMAJTT -M GTRGAMMA -o speciesA

    2.Tutorial download

    Users could download the tutorial here.

    Contact us

    Mr. Wei Dong, 1369852697@qq.com
    Dr. Fei Chen, 810569243@qq.com

    Cite us

    1. URL: eplant.org/speciestree.html
    2. Reference: please wait for the reference for SpeciesTree