MACSE pipeline

MACSE specifications

Information


Unique identifier OMICS_10019
Name MACSE
Alternative name Multiple Alignment of Coding SEquences
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data Coding nucleotide sequences
Output data MACSE aligns coding nucleotide sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons.
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License CeCILL version 2.1
Computer skills Advanced
Version 1.01
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Vincent Ranwez <>

Information


Unique identifier OMICS_10019
Name MACSE
Alternative name Multiple Alignment of Coding SEquences
Interface Web user interface
Restrictions to use None
Input data Coding nucleotide sequences
Output data MACSE aligns coding nucleotide sequences with respect to their AA translation while allowing NT sequences to contain multiple frameshifts and/or stop codons.
Programming languages Java
Computer skills Basic
Version 1.01
Stability Stable
Maintained Yes

Maintainer


  • person_outline Vincent Ranwez <>

Publication for Multiple Alignment of Coding SEquences

MACSE citation

2015
PMCID: 4540973

[…] crassa database) were aligned to de novo assemblies using blast+ (basic local alignment search tool) (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/bla st+/). het domain sequences were aligned using macse (ranwez et al. 2011). multiple alignments were visualized using jalview (http://www.jalview.org). genome assemblies of n. tetrasperma, n. discreta, and p. anserina were obtained from the u.s. […]

MACSE institution(s)
Institut des Sciences de l'Evolution, UMR5554-CNRS, Université Montpellier II, Montpellier, France
MACSE funding source(s)
This work was supported by the French Agence Nationale de la Recherche “Domaines Emergents” (ANR-08-EMER-011, “PhylAriane”), the Centre National de la Recherche Scientifique (PEPS-INSB-2010), and the Montpellier Bioinformatics Biodiversity platform (MBB).

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