DAMBE

DAMBE, which stands for  Data Analysis in Molecular Biology and Evolution, is a small, easy to use application specially designed to help you with data analysis and molecular biology and evolution.

You can use this application to help you with sequence alignment in various manners, such as using it for general sequence alignment with amino acid and nucleotide sequences or for aligning sequences of protein-coding nucleotide against aligned amino acid ones.

It can help you with distance-based methods such as neighbor-joining, UPGMA, FastME or Fitch-Margoliash in combination with various genetic distances that include "simultaneously-estimated maximum composite likelihood distances" but also various distances that are based on amino acid, nucleotide and codon-based substitution models.

You'll be able to determine estimations of proportions for invariant sites or the shape value "of the gamma distribution for rate heterogeneity," find substitution models that fit the best and even test substitution saturation.

DAMBE can be easily installed on the target computer, since it's only necessary to run the setup executable and follow the on-screen instructions provided by the integrated wizard component, as the rest of the process is carried out automatically, without further assistance on your side.