README.md

Introduction

dN/dS ratio estimates of mites using Codeml (PAML).

The input data don't work with Codeml.

Alignments are in phylip format.

Trees have been generated with RAxML but have to be reformatted depending on the model.

mites2codeml.py is useful to reformat the input data to make it compatible with Codeml (PAML).

Table of contents

1. Required files
2. dN/dS ratio estimates

1) Required input

1. Need 2 directory and 1 control file:

   • alignments/ directory: contain alignments in phylip format.
   • branch_lengths/ directory: contain the RAxML's trees in newick format.
   • control template (available here codeml_[model].ctl)

2) dN/dS ratio estimates

1. Create a directory for your species (mites).

mkdir mites

Copy the 3 required input into this directory.

ll mites

total 9
drwxr-xr-x 2 ptranvan dee_schwan 3545  2 mar 11:00 alignments
drwxr-xr-x 2 ptranvan dee_schwan 3545  2 mar 11:01 branch_lengths
-rw-r--r-- 1 ptranvan dee_schwan 2931  2 mar 11:00 codeml_[model].ctl

mites2codeml.py can be stored anywhere but has to be run from the mites directory.

2.1) For SAI and TI models:

cd mites

python path/to/mites2codeml.py -s sai_ti -i1 alignments -i2 branch_lengths -i3 codeml_sai_ti.ctl -e <your_email> -o sai_ti.sh

2.2) For Hydrophobicity model:

cd mites

python path/to/mites2codeml.py -s hydrophobicity -i1 alignments -i2 branch_lengths -i3 codeml_hydrophobicity.ctl -e <your_email> -o hydrophobicity.sh

3. A script (*.sh) will be created. It has to be run on Vital-IT server ([email protected]):

chmod +x *.sh
./*.sh

Once done, a directory output will be created.

4. Options:

-i1: alignments directory.
-i2: branch_lengths directory.
-i3: control file.
-e: email for job confirmation.
-o: name of the script file to be executed.