ChangeLog

2010-12-09  1.3-RELEASE

* Use CMake for compilation and installation
* New scaling option enabled by default (identical sequences default to cost of 0)
* Protein evolutionary models: aazeta and aageo
* Fasta and Phylip format output support
* Clustal and Phylip format input support
* Report sequence identity measure
* Matrix output formats for distance measures
* Look for "ngilarc" file in the home directory.
* New separator option
* New const-align option
* Replace arg-file option with ngilarc option.
* Use custom zeta function if GSL not found.
* Optimize size of travel table.

* Ordering of --pairs-all fixed
* bug fix for output of large alignments >10kb
* minor bug fix for geo model


2007-08-23  1.2.1-RELEASE

* Fixed two bugs related to alignment printing

2007-08-22  1.2-RELEASE

* Changed license to GPL
* Reorganized source code to a more modular framework.
* Compiling from source now requires GSL and Boost Libraries
* Added two evolutionary models: K2P+Zeta and K2P+Geometric
* Command line options changed 
* Only FASTA supported for input
* Tie breaking has changed
* The Clustal output format has been altered
* Man page updated and tied to cmds file
* Added pairs setting for more control of sequential alignments
* Several Bug fixes

2007-02-23  1.1-RELEASE

* Added options to specify free-end gap scores
* Fixed bug with holisitc algorithm

2006-10-26  1.0-RELEASE

* Initial Release