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RAxML Next Generation with parallel computation of Transfer Bootstrap Expectation (TBE) scores and computation of TBE extra information

Introduction

Greetings! If you are not here for parallel computation of TBE support or computation of the TBE extra information, we strongly advise you to use the most up-to-date version of RAxML-NG instead. It can be found here: https://github.com/amkozlov/raxml-ng

Computing TBE support with extra information

Here is one example call which computes TBE support scores as well as the extra table and the extra array. It uses the cutoff value 0.3 for that. It uses 10 threads:

./raxml-ng --support --tree REF.nw --bs-trees BS.nw --bs-metric TBE --extra tbe_extra_table,tbe_extra_array,tbe-cutoff{0.3} --threads 10

If you don't understand what this is, please read our paper at https://www.biorxiv.org/content/10.1101/734848v2

Installation instructions

  • For most desktop Unix/Linux and macOS systems, the easiest way to install RAxML-NG is by using the pre-compiled binary:
    Download 64-bit Linux binary
    Download 64-bit OSX/macOS binary

  • For clusters/supercomputers (i.e., if you want to use MPI), please use the following installation package which contains pre-built libpll. You will need GCC 6.4+ and CMake 3.0.2+ in order to compile RAxML-NG for your system.
    Download RAxML-NG-MPI for Linux

  • Binaries for Windows will become available later on

  • If neither of the above options worked for you, please clone this repository and build RAxML-NG from scratch.

  1. Install the dependecies. On Ubuntu (and other Debian-based systems), you can simply run:
sudo apt-get install flex bison libgmp3-dev

For other systems, please make sure you have following packages/libraries installed:
GNU Bison Flex GMP

  1. Build RAxML-NG.

PTHREADS version:

git clone --recursive https://github.com/amkozlov/raxml-ng
cd raxml-ng
mkdir build && cd build
cmake ..
make

MPI version:

git clone --recursive https://github.com/amkozlov/raxml-ng
cd raxml-ng
mkdir build && cd build
cmake -DUSE_MPI=ON ..
make

Portable PTHREADS version (static linkage, compatible with old non-AVX CPUs):

git clone --recursive https://github.com/amkozlov/raxml-ng
cd raxml-ng
mkdir build && cd build
cmake -DSTATIC_BUILD=ON -DENABLE_RAXML_SIMD=OFF -DENABLE_PLLMOD_SIMD=OFF ..
make