Tag: MUSCLE

RNAlign2D – Multiple Sequence Alignment of RNA using MUSCLE and Secondary Structure data

RNAlign2D

:: DESCRIPTION

RNAlign2D is a Python wrapper allowing one to align multiple RNA molecules using information about secondary structure and sequence. For this purpose MUSCLE program is used, but one can adjust it to use any other multiple sequence alignment tool.

::DEVELOPER

RNA Bioscience Initiative

:: REQUIREMENTS

  • Linux / MacOsX
  • Python
  • MUSCLE

:: DOWNLOAD

RNAlign2D

:: MORE INFORMATION

Citation

Woźniak T, Sajek M, Jaruzelska J, Sajek MP.
RNAlign2D: a rapid method for combined RNA structure and sequence-based alignment using a pseudo-amino acid substitution matrix.
BMC Bioinformatics. 2021 Oct 16;22(1):504. doi: 10.1186/s12859-021-04426-8. PMID: 34656080; PMCID: PMC8520625.

MUSCLE 3.8.31 – Multiple Sequence Alignment

MUSCLE 3.8.31

:: DESCRIPTION

MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options is provided that give you the choice of optimizing accuracy, speed, or some compromise between the two. Default parameters are those that gave the best average benchmark accuracy in my tests. However, benchmark accuracy is a rather dubious measure

MUSCLE Online version

::DEVELOPER

Robert Edgar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX

:: DOWNLOAD

MUSCLE

:: MORE INFORMATION

Citation

Edgar, R.C. (2010)
Quality measures for protein alignment benchmarks
Nucleic Acids Res., 2010, 1–9.

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