Version 2.7.1

This release supports the new Apple Mx (ARM) chips and Linux (ARM) chips.

Major Features:

• A new option -l is added to assign the starting rate matrix.
• Detailed README has been added.
• Updated user manual.
• Updated license file.
• Bug fixes to improve software stability.

Note: The way to compile the source codes has been changed. Please refer to the README.

Usage of the option -l for assigning the starting rate matrix.

-l <start matrix>   : The rate matrix to start from. It is not a file,
                        but a string representing the rate matrix.
                        For example: -l 1,1,1,1,1,2,1,1,2,2,2,2,2,2

For example:

./HAL2 data.phy tree.txt -l 1,1,1,1,1,2,1,1,2,2,2,2,2,2

The above command starts the iteration from the rate matrix: 1,1,1,1,1,2,1,1,2,2,2,2,2,2