How to configure plugins

There are two ways to configure the plugins:

1. Download PhyloSuite with plugins

When using Windows and Mac OSX systems, you can download PhyloSuite_xxx_Win32/64_with_plugins.rar and PhyloSuite_xxx_Mac_with_plugins.zip from https://github.com/dongzhang0725/PhyloSuite/releases, respectively. All plugins, except Python 2.7, Perl 5, Java, Rscript, HmmCleaner and trimAl (MAC) are included.

2. Configure plugins separately

Interpretation of the install state.

If Python 2.7, Perl 5, Java (JRE > 1.5), HmmCleaner.pl and trimAl have been installed and added to the environment variable ($PATH), they will be automatically detected by PhyloSuite. Open the plugin settings window via Settings-->Settings in the menu bar. There are two ways to configure your plugins:

2.1. Specify executable file

When you have the plugins already installed on your computer, you can just specify the paths directly.

  1. Click the Install button of each plugin to open the configuration window;
  2. In the Specify box, click Add button to select files;
  3. Select the executable file (see the table below);
  4. Select Open;
  5. Click Ok.
Programs Executable File (Win) Executable File (MAC) Executable File (Linux)
MAFFT v7.313 path-to-MAFFT/mafft-win/mafft.bat path-to-MAFFT/mafft-mac/mafft.bat path-to-MAFFT/bin/mafft or
/usr/bin/mafft
Java (JRE > 1.5) path-to-Java/java.exe path-to-Java/java or usr/bin/java path-to-Java/java or usr/bin/java
MACSE v2.01b path-to-MACSE/macse_v2.03.jar path-to-MACSE/macse_v2.03.jar path-to-MACSE/macse_v2.03.jar
IQ-TREE v. 1.6.8 path-to-IQ-TREE/bin/iqtree.exe path-to-IQ-TREE/bin/iqtree path-to-IQ-TREE/bin/iqtree
MrBayes 3.2.6 path-to-MrBayes/mrbayes_x64.exe or
path-to-MrBayes/mrbayes_x86.exe
path-to-MrBayes/mb path-to-MrBayes/bin/mb
PartitionFinder2 path-to-PartitionFinder2/partitionfinder-2.1.1 path-to-PartitionFinder2/partitionfinder-2.1.1 path-to-PartitionFinder2/partitionfinder-2.1.1
Gblocks 0.91b path-to-Gblocks/Gblocks.exe path-to-Gblocks/Gblocks path-to-Gblocks/Gblocks
trimAl path-to-trimAl/trimal.exe path-to-trimAl/trimal or usr/bin/trimal path-to-trimAl/trimal or usr/bin/trimal
Perl 5 path-to-Perl/perl.exe path-to-Perl/perl or usr/bin/perl path-to-Perl/perl or usr/bin/perl
HmmCleaner.pl path-to-HmmCleaner/HmmCleaner.pl path-to-HmmCleaner/HmmCleaner.pl or usr/bin/HmmCleaner.pl path-to-HmmCleaner/HmmCleaner.pl or usr/bin/HmmCleaner.pl
Rscript 3.4.4 path-to-R/bin/Rscript.exe path-to-R/bin/Rscript path-to-R/bin/Rscript
Python 2.7 path-to-Python2.7/python.exe path-to-Python2.7/bin/python path-to-Python2.7/bin/python
tbl2asn path-to-tbl2asn/win.tbl2asn/tbl2asn.exe not allowed not allowed
MPICH2 not allowed not allowed path-to-MPICH2/bin/mpiexec or
path-to-MPICH2/bin/mpirun

2.2. Download plugins automatically

PhyloSuite also allows user to download the plugins and configure them automatically. Just click the Download button, and the plugin will be downloaded and installed on your computer automatically.

However, for Rscript and Python 2.7, there are two additional steps:

  1. When they are downloaded, you need to select a folder to install them;
  2. Next you need to specify the executable files, as described in Section 1.
    Rscript:

    Python 2.7:

In addition, if the plugin download fails, you can download and install them manually, via a link provided directly below (click “here”). Once downloaded, unzip them to your computer and specify the path.

2.3. PartitionFinder configuration

As PartitionFinder2 Python script relies on Python 2.7, and additional six dependencies should be configured, we have compiled PartitionFinder2 (MAC and Windows only) so it does not rely on Python 2.7 any more.

  1. Open PartitionFinder2 configuration window;
  2. Click Download button in the Install compiled PartitionFinder2 box to download and install PartitionFinder2 automatically.

You may also select to install Python 2.7 and PartitionFinder2 Python script:
PartitionFinder2

  1. Open PartitionFinder2 configuration window;
  2. Click Download button in the Install python 2.7 and PartitionFinder2 box to download and install it automatically.

Python 2.7

  1. Open Python 2.7 configuration window;
  2. Click Download button in the Download box to download Anaconda2. For the additional steps to complete the Python 2.7 configuration please refer to Section 2.

    Note: Anaconda Python distribution will download for Python 2.7 (because it contains all of the dependencies required by PartitionFinder2: numpy, pandas, pytables, pyparsing, scipy and sklearn). As it is around 500M in size, your download may take some time. That’s why we recommend that you download the compiled PartitionFinder2, which does not require Python 2.7.
2.3.1. Troubleshooting

If you specify the path to Python 2.7 pre-installed on your computer, sometimes you may encounter the error below, indicating the absence of the six dependencies.

There are three solutions:

  1. Install compiled PartitionFinder2 (recommended, MAC and Windows only);
  2. Install Anaconda2 and specify the python executable file, as shown above;
  3. Install these six dependencies to Python 2.7:
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    pip install pandas
    pip install numpy
    pip install tables
    pip install pyparsing
    pip install scipy
    pip install sklearn

2.4. HmmCleaner configuration

HmmCleaner relies on HMMER, Perl 5 and a lot of dependencies. Therefore, some users may have difficulty in configuring it. Here we make a brief tutorial for the configuration of HmmCleaner.

2.4.1. Configuration of HMMER
  1. If you already have conda installed, you can install HMMER via conda install -c bioconda hmmer or conda install -c bioconda/label/cf201901 hmmer command.
  2. If you don’t have Conda, you need to download and install HMMER here: http://hmmer.org.

Please Note that all executables from HMMER have to be added in the environment variable ($PATH).

2.4.2. Configuration of Perl and dependencies installation

Here I recommend Perl version 5.18.0, as I experienced failure in installing dependencies in version 5.26.

When perl is installed, you can use cpanm to install HmmCleaner:

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cpan App::cpanminus
cpanm Bio::MUST::Apps::HmmCleaner --force

Alternatively, you can also install HmmCleaner following this instruction: https://metacpan.org/source/ARNODF/Bio-MUST-Apps-HmmCleaner-0.180750/INSTALL

It may take some times to install, if it installs successfully, HmmCleaner.pl will be automatically add to the environment variables. Then you need to close and reopen PhyloSuite to see if it installed successfully (if you see Uninstall button, it means success).

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