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RAxML-NF

This repository contains:

1) A dataset containing motor protein Prestin from 35 different species, as published by Liu et al.15. Motor protein Prestin is expressed in mammalian outer hair cells (OHCs) and is thought to confer high frequency sensitivity and selectivity in the mammalian auditory system.

2) Results of RAxML estimated phylogenetic trees run on Mac, Linux and with Nextflow portable runtime.

3) The instructions how to replicate these results.

Folder structure

  • Folder data/: input dataset.

  • Folder RAxML_NF_RESULTS/: experiment results.

How to replicate results

Clone this repository from GitHub using the following command:

git clone https://github.com/cbcrg/raxml-nf.git

then move in the directory raxml-nf create by the clone command.

Native RAxML run on Linux & Mac

Download the RAxML toolset for Linux from
this link,

Compile typing:

make -f Makefile.gcc

and install it properly, making sure that the raxmlHPC binary is in a directory in your PATH.

You can then run RAxML using the following command:

raxmlHPC -p 9 -T 2 -f d -j -m PROTGAMMALG -s data/prestin_SLC26A5.35eutheria.original.msa -n PRESTIN 

Nextflow RAxML run on Linux & Mac

Install Nextflow with the following command:

export NXF_VER=0.22.0
curl -fsSL get.nextflow.io | bash

Install Docker following the instruction at this page.

Clone this repository and change in the project root directory as shown below:

git clone https://github.com/cbcrg/raxml-nf.git && cd raxml-nf

Pull the required Docker image with this command:

docker pull cbcrg/raxml-nf@sha256:308d687223753a8b80588c05aeef8f344aefc3db2195e2676d37a2a36b6dbdbb

Finally launch RAxML with Nextflow by using the following command:

nextflow run raxml.nf -with-docker

The command above executes RAxML using the default parameters specified in the native
command line provided in the previous example and the docker image specified above.

If you wish to run RAxML with Nextflow without docker, make sure the raxmlHPC binary is in your PATH and then run the following command:

nextflow run cbcrg/raxml-nf 
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