Efficient Implied Alignment

This repository hosts the program implied-align implementing the algorithm described in the paper Efficient Implied Alignment and a script to replicate the results of the paper.

Installation of implied-align

You can build and install implied-align from source using the Haskell build system ghcup via the supplied makefile from the source directory of this project:

$ make install

After the make install command has completed, the implied-align binary will be placed in this project's bin directory.

Running implied-align

The implied-align program takes a number of command line arguments to specify inputs and outputs. For more information run the following command:

$ implied-align --help

Replicating results of the paper

For convenience of replicating the results of the paper, a "replicate-results" script has been provided. All that is need to replicate the paper's results is to run the following command:

$ make replicate

This will create a replicate-results directory, with sub directories csv, data, img, taxa, and tree.

• The taxa directory holds temporary files used in pruning the data-sets.
• The data & tree directories hold the pruned input files for the data-sets.
• The csv directory holds the timing information measured during the replication of the results.
• The img directory holds the generated images from the results.