It has been a long time coming, but I have finally released Ngila 1.3. This version fixes a few bugs and includes many new features.
- 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
