run_phyml_batch

A toolkit to perform nucleotide and amino acid sequence phylogenetic analysis via PhyML_v3.3 and produce the pairwise distance matrix

Description

This toolkit can be run phyml program in batch in a directory. It requires Python 3 and PhyML (v3.3). it will output the estimated ML tree file as well as the pairwise distance matrix for each input sequence alignment file.

Usage

1. Clone this repository in your working directory

git clone https://github.com/MullinsLab/run_phyml_batch.git

• it will create a directory called "run_phyml_batch" in your working directory

2. Download PhyML in your designated directory

 git clone -b v3.3.20220408 https://github.com/stephaneguindon/phyml.git phyml_v3.3.20220408

• the current release is v3.3.20220408
• it will create a directory called "phyml_3.3.20220408"

3. Update files in order to output pairwise distances after running phyml

cd phyml_v3.3.20220408/src
python your_working_director/run_phyml_batch/script/updatefiles.py
cd ..

4. In the directory of phyml_v3.3.20220408/, install phyml following the instructions on phyml GitHub

5. Modify phyml_path.py to set the correct path to run phyml in your computer

• open phyml_path.py in the directory your_working_director/run_phyml_batch/script/ in a text editor
• replace "where_your_phyml_path/program_name" with the correct phyml path where you just installed, e.g "your_designated_directory/phyml_v3.3.20220408/src/phyml" (the path should include the program name), and save the file

6. In the directory where the input sequence alignments are, run phyml on each sequence alignment file (must be with .fasta extension) to output tree and distance matrix

cd directroy_where_inputs_are/
python your_working_director/run_phyml_batch/script/run_phyml.py -t datatype -p numberOfProcessors

• you have to provide the value of datatype (nt for nuclotide sequences, aa for amino acid sequences)
• the default value of numberOfProcessors is 1. You can run multiprocessors by providing the value > 1 based on your computer settings
• it will output estimated ML trees in nuwick and pairwise distance matrix for each input file, and a log subdirectory storing the log message of running the toolkit