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PASTA (Practical Alignment using Sate and TrAnsitivity) is a multiple sequence alignment tool that uses a guide tree.


Sequence analysis; Protein interactions


  • Operation: Multiple sequence alignment
  • Input: FASTA
  • Output: Alignment; tree
  • Software interface: Command-line user interface; graphical user interface
  • Language: Python;Java
  • Operating system: Linux; Mac OS X
  • License: GNU General Public License v3
  • Cost: Free
  • Version name: 1.8.3
  • Maturity: Stable
  • Credit: The National Science Foundation (NSF) grant DBI 0733029 to T.W., by the Howard Hughes Medical Institute (HHMI) International Predoctoral Fellowship to S.M., and by a subgrant from the University of Alberta to T.W., made possible through a donation from Musea Ventures, which is held by Professor Gane Ka-Shu Wong. This work was also supported by a generous allocation from TACC and by the iPlant Collaborative, NSF grant DBI-1265383. L.W. and S.G. were supported by NSF grant 0331453; L.W. was supported in part by the National Institutes of Health (NIH) through grants T32-HG000046, NIA U24-AG041689, and R01-GM099962. J.K.'s participation in this project was funded, in part, by a Health Research Formula Fund from the Pennsylvania Department of Health
  • Contact: warnow _at_
  • Collection: -


Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T "PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences" J Comput Biol. 2015 May;22(5):377-86.
PMID: 25549288
PMCID: PMC4424971

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