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update README and download links
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amkozlov committed May 9, 2023
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Expand Up @@ -16,14 +16,14 @@ Documentation: [github wiki](https://github.com/amkozlov/raxml-ng/wiki)
## 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**](https://github.com/amkozlov/raxml-ng/releases/download/1.1.0/raxml-ng_v1.1.0_linux_x86_64.zip)
[**Download 64-bit OSX/macOS binary**](https://github.com/amkozlov/raxml-ng/releases/download/1.1.0/raxml-ng_v1.1.0_macos_x86_64.zip)
[**NEW (experimental!): Apple M1 binary**](https://github.com/amkozlov/raxml-ng/releases/download/1.1.0/raxml-ng_v1.1.0_macos_M1_experimental.zip)
[**Download 64-bit Linux binary**](https://github.com/amkozlov/raxml-ng/releases/download/1.2.0/raxml-ng_v1.2.0_linux_x86_64.zip)
[**Download 64-bit OSX/macOS binary**](https://github.com/amkozlov/raxml-ng/releases/download/1.2.0/raxml-ng_v1.2.0_macos_x86_64.zip)
[**Download Apple M1 binary**](https://github.com/amkozlov/raxml-ng/releases/download/1.2.0/raxml-ng_v1.2.0_macos_M1_experimental.zip)

* 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**](https://github.com/amkozlov/raxml-ng/releases/download/1.1.0/raxml-ng_v1.1.0_linux_x86_64_MPI.zip)
[**Download RAxML-NG-MPI for Linux**](https://github.com/amkozlov/raxml-ng/releases/download/1.2.0/raxml-ng_v1.2.0_linux_x86_64_MPI.zip)

* On Windows, you can use [linux binary](https://github.com/amkozlov/raxml-ng/releases/download/1.1.0/raxml-ng_v1.1.0_linux_x86_64.zip) via [Windows Subsystem for Linux](https://ubuntu.com/wsl), but performance might be lower than with native Linux execution.
* On Windows, you can use [linux binary](https://github.com/amkozlov/raxml-ng/releases/download/1.2.0/raxml-ng_v1.2.0_linux_x86_64.zip) via [Windows Subsystem for Linux](https://ubuntu.com/wsl), but performance might be lower than with native Linux execution.

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

Expand Down Expand Up @@ -77,11 +77,11 @@ If still in doubt, please feel free to post to the [RAxML google group](https://

## Usage examples

1. Perform single tree inference on DNA alignment
(random starting tree, general time-reversible model, ML estimate of substitution rates and
1. Perform single quick&dirty tree inference on DNA alignment
(one parsimony starting tree, general time-reversible model, ML estimate of substitution rates and
nucleotide frequencies, discrete GAMMA model of rate heterogeneity with 4 categories):

`./raxml-ng --msa testDNA.fa --model GTR+G`
`./raxml-ng --search1 --msa testDNA.fa --model GTR+G`

2. Perform an all-in-one analysis (ML tree search + non-parametric bootstrap)
(10 randomized parsimony starting trees, fixed empirical substitution matrix (LG),
Expand Down Expand Up @@ -120,6 +120,8 @@ doi:[10.1093/bioinformatics/btz305](https://doi.org/10.1093/bioinformatics/btz30
* Benoit Morel
* Ben Bettisworth
* Sarah Lutteropp
* Julia Haag
* Anastasis Togkousidis

## References

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