# 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/di

                        amond-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_i86linu

                        x64.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")

                    

                        $ 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

                        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 commaseparated

                        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

                    

2.Tutorial download