Requirements for fastphylo:

* cmake (>= 3.18)
* a C++17 compiler
* BLAS and LAPACK development libraries (required - used by fastprot's
  maximum-likelihood code). On Linux: e.g. "apt install libblas-dev
  liblapack-dev". On macOS: none needed, Apple's Accelerate framework
  is found automatically.
* Eigen3 (required - used by fastprot's maximum-likelihood code for
  its dense 20x20 matrix operations). Header-only. On Linux: e.g.
  "apt install libeigen3-dev". On macOS: "brew install eigen". Via
  vcpkg: already listed in vcpkg.json as "eigen3".
* libxml2 development libraries (optional - enables XML input/output
  in fastprot/fastdist/fnj). On Linux: e.g. "apt install libxml2-dev".
  On macOS: none needed, the system's own libxml2 is found
  automatically. If not found, cmake prints a warning and builds
  without XML support rather than failing - pass -DWITH_LIBXML=OFF to
  build without it intentionally and silence the warning.
* simde (only if building on a non-x86 CPU, e.g. Apple Silicon or ARM
  Linux - not needed on x86_64/i386). E.g. "brew install simde" or
  "apt install libsimde-dev".

If you want to build the distributed version of fastprot, fastprot_mpi, you also need:

* openmpi (or equivalent), and set the CMAKE flag BUILD_WITH_MPI

Unfortunately, the MPI version does not build without tinkering on all platforms. It has worked for
us on Ubuntu/Debian using standard packages and on macOS using HomeBrew packages.

If you want to build the documentation (auto-generated examples, yielding up-to-date help-texts, it is a feature!),
then you also need:

* xmlto (only for -DBUILD_DOCROOT=ON)
* lxml, the Python library


This package uses the program cmake for building and packaging the software.
To install into the directory $HOME/bin run these commands:

  mkdir $HOME/bin
  cd fastphylo
  mkdir build
  cd build
  cmake -DCMAKE_INSTALL_PREFIX=$HOME/bin ..
  make
  make install

Without the installation prefix option, cmake installs into the
default path (may be /usr/local/bin).

If you want to build and install fastprot_mpi, remember to use the option
  -DBUILD_WITH_MPI=ON
in the cmake command.

If you want to install the documentation too, you need to add the flag
  -DBUILD_DOCBOOK=ON
to the cmake command line.



