From fd32e7f73c3ee44c526c7555a8d04e84b03bd51c Mon Sep 17 00:00:00 2001 From: Alexey Kozlov Date: Tue, 9 May 2023 21:51:51 +0200 Subject: [PATCH] update README and download links --- README.md | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index f1f8581d..190dcf57 100644 --- a/README.md +++ b/README.md @@ -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. @@ -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), @@ -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