ALTER (ALignment Transformation EnviRonment) is a public tool for MSA (Multiple Sequence Alignment) file format conversion. It performs a program-oriented conversion between different DNA and protein MSA formats.


In order to develop this server, we first identified the most popular tools for the evolutionary analysis of MSAs, and examined their particular format requisites. Once the specific conversion was implemented, it was validated in order to guarantee that the generated MSA could be read without problem by the application and the intended operating system. Our intention and compromise is to maintain and extend these lists following user suggestions. In addition, ALTER is able to “collapse” sequences to haplotypes –unique sequences–, indicating which sequence corresponds to which haplotype. Eliminating this redundancy can be very helpful, for example, to speed up phylogenetic analyses.

Currently, the list of supported programs includes:

  • Clustal
  • T-Coffee
  • jModelTest
  • MrBayes
  • PAML
  • PAUP
  • PhyML
  • ProtTest
  • RAxML
  • TCS

The allowed standard formats are:

  • ALN
  • GDE
  • MEGA
  • MSF
  • PIR 

Visit the Site



Visit our repositories on

2019 Sistemas Informáticos de Nueva Generación