ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments

Biochem Biophys Res Commun. 2012 Mar 23;419(4):779-81. doi: 10.1016/j.bbrc.2012.02.101. Epub 2012 Feb 27.


Constructing multiple homologous alignments for protein-coding DNA sequences is crucial for a variety of bioinformatic analyses but remains computationally challenging. With the growing amount of sequence data available and the ongoing efforts largely dependent on protein-coding DNA alignments, there is an increasing demand for a tool that can process a large number of homologous groups and generate multiple protein-coding DNA alignments. Here we present a parallel tool - ParaAT that is capable of parallelly constructing multiple protein-coding DNA alignments for a large number of homologs. As testified on empirical datasets, ParaAT is well suited for large-scale data analysis in the high-throughput era, providing good scalability and exhibiting high parallel efficiency for computationally demanding tasks. ParaAT is freely available for academic use only at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Humans
  • Mice
  • Pan troglodytes
  • Proteins / genetics*
  • Sequence Alignment / methods*
  • Sequence Analysis, DNA / methods*
  • Software*


  • Proteins