New upstream version 3.3.20190321

*.i*86

*.x86_64

*.hex

Makefile.in

config.guess*

config.sub*

config.h.in

aclocal.m4

compile

configure

depcomp

install-sh

missing

autom4te.cache

*~

doc/html

doc/latex

\#*#

ltmain.sh

m4/*.m4

*.orig

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//////////////////////////////////////////////////////////////////////////////////////////////////////

// You downloaded a stable release  of PhyML from https://github.com/stephaneguindon/phyml/releases //

//////////////////////////////////////////////////////////////////////////////////////////////////////

### 1. You downloaded a stable release  of PhyML from [here](https://github.com/stephaneguindon/phyml/releases) 

To install any program that is part of the PhyML package, type the following commands:

```bash

./configure --enable-XXXX;

make;

```

where XXXX is phyml or phyrex or phytime.

To compile a Windows executable, install MinGW and run:

```bash

./configure --enable-win --enable-XXXX;

make;

```

To install the MPI version of PhyML, type the following commands:

```bash

autoreconf -i;

./configure --enable-mpi --enable-phyml;

make;

```

If you are using a Mac computer, you will need to install the package pkg-config. The

following command should set you up (provided Homebrew is installed on your Mac...):

brew install pkg-config; Next, typing './configure --enable-XXXX; make;' should generate

the phyml binary in the src/ directory.

brew install pkg-config; Next, typing `./configure --enable-XXXX; make;` should generate

the phyml binary in the `src/` directory.

//////////////////////////////////////////////////////////////////////////

//                    You have cloned PhyML from GitHub                 //

//////////////////////////////////////////////////////////////////////////

### 2. You cloned PhyML from GitHub

To install any program that is part of the PhyML package, type the following command:

```bash

sh ./autogen.sh;

```

If you are using a Mac computer or running a Unix-like operating system, you will need 

to install the packages autoconf automake and pkg-config. On a Mac, the following command 

should set you up (provided Homebrew is installed on your Mac...): brew install pkg-config

autoconf automake;

Next, typing './configure --enable-XXXX; make;' should generate the phyml binary in the src/

Next, typing `./configure --enable-XXXX; make;` should generate the phyml binary in the src/

directory, where XXXX is phyml or phyrex or phytime.