<commit_before>#Overview
Empar is a package based on the EM algorithm for parameter estimation in discrete-time Markov models:


### Dependencies

The package used version 1.47.0 of the [boost] library for parts of the code involving maths and random generation (downloaded from: [boost source]). As such, use, modification and distribution are subject to the Boost Software License, Version 1.0. (See [boost license]).

### Compilation and command line use
To compile this code you need a development environment with the GNU gcc compiler ('make').

```
empar <tree file> <fasta file> <model>
```
where
*  *tree file*   [Newick] tree (not necessarily bifurcated)
*  *fasta file*  [fasta] input alignment 
*  *model*       model: jc, k80, k81, ssm.
e.g.
```
./Empar test.tree data.fa ssm,
```<commit_msg>readme shortened<commit_after>#Overview
**Empar** is an implementation of an MLE method based on the EM algorithm for effective estimation parameters of the (discrete-time) Markov evolutionary models.

### Dependencies

The package used version 1.47.0 of the [boost] library for parts of the code involving maths and random generation (downloaded from: [boost source]). As such, use, modification and distribution are subject to the Boost Software License, Version 1.0. (See [boost license]).

### Compilation and command line use
To compile this code you need a development environment with the GNU gcc compiler ('make').

```
empar <tree file> <fasta file> <model>
```
where
*  *tree file*   [Newick] tree (not necessarily bifurcated)
*  *fasta file*  [fasta] input alignment 
*  *model*       model: jc, k80, k81, ssm.
e.g.
```
./Empar test.tree data.fa ssm,
```
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