MCALIGN protocols

MCALIGN computational protocol

MCALIGN specifications


Unique identifier OMICS_03699
Alternative name MCALIGN2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A sequence
Input format FASTA
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License Other
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Peter Keightley <>
  • person_outline Toby Johnson <>

Publications for MCALIGN

MCALIGN IN pipeline

PMCID: 2174951
PMID: 17976238
DOI: 10.1186/1471-2148-7-208

[…] and if there were no other introns within 5 amino acids of this position on either side. a total of 730 pairs of intron were identified by this approach., intronic dna sequences were aligned using mcalign2, which aligns noncoding dna sequences based on explicit models of indel evolution [17]. to infer an appropriate indel frequency model, we first aligned the dataset with an indel model […]

MCALIGN institution(s)
Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
MCALIGN funding source(s)
Supported by Dorothy Hodgkin Postgraduate Studentship Award and by the Biotechnology and Biological Sciences Research Council grant #206/D 16977.

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