MACSE statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MACSE
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Tool usage distribution map

This map represents all the scientific publications referring to MACSE per scientific context
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Associated diseases

This word cloud represents MACSE usage per disease context
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Popular tool citations

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Protocols

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 2
Stability Stable
Maintained Yes

Versioning


No version available

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

Publications for Multiple Alignment of Coding SEquences

MACSE citations

 (80)
library_books

NS1 codon usage adaptation to humans in pandemic Zika virus

2018
PMCID: 5942634
PMID: 29768530
DOI: 10.1590/0074-02760170385

[…] enBank (www.ncbi.nlm.nih.gov/genbank/) that had information of year and country of isolation (alignment available from: https://github.com/CaioFreire/CUB). First, we aligned the coding sequences with MACSE program v0.9 (https://bioweb.supagro.inra.fr/macse/) and curated it with AliView v1.171 (http://ormbunkar.se/aliview/). Since we previously found evidence for recombination in ZIKV from Africa ( […]

call_split

Macroecology and macroevolution of the latitudinal diversity gradient in ants

2018
Nat Commun
PMCID: 5934361
PMID: 29725049
DOI: 10.1038/s41467-018-04218-4
call_split See protocol

[…] provide a summary here and the full phylogenetic methods in Supplementary Note . We consolidated sequence data from recent studies–, , – (Supplementary Data ), aligned a set of 11 nuclear loci using MACSE and MAFFT, and set nucleotide substitution and clock models using Partition Finder and ClockstaR. We reconstructed a set of dated backbone trees using a combination of RaxML and BEAST2 and a dat […]

library_books

Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi

2018
Sci Rep
PMCID: 5897359
PMID: 29651164
DOI: 10.1038/s41598-018-24301-6

[…] e 3,060 groups were selected by parsing the ortholog groups (OGs) derived above, and keeping only single-copy genes (i.e., had no evidence of duplication) in all 13 taxa. Sequences were aligned using MACSE, with default parameters. MACSE alignments were processed to remove all codons including sites with a gap in at least one of the samples, and then concatenated. Node ages were estimated using a […]

library_books

Genome wide identification of natural RNA aptamers in prokaryotes and eukaryotes

2018
Nat Commun
PMCID: 5876405
PMID: 29599443
DOI: 10.1038/s41467-018-03675-1

[…] high sensitivity, we changed the default blastn parameters as follows: “-e 1e-5 -word_size 7 –gapopen 2 –gapextend 1”. We aligned the noncoding sequences using MUSCLE, and the coding sequences using MACSE, to construct the multiple sequence alignment. The nucleotide substitution rate of riboswitches, 3′ UTR and 5′ UTR were calculated using Kimura’s 2-parameter method. The synonymous and non-synon […]

library_books

Phylogenomics of palearctic Formica species suggests a single origin of temporary parasitism and gives insights to the evolutionary pathway toward slave making behaviour

2018
BMC Evol Biol
PMCID: 5872393
PMID: 29592795
DOI: 10.1186/s12862-018-1159-4

[…] . cinerea) with transcriptomes available from a recent article []. We used OrthoMCL [] to retrieve 945 one-to-one ortholog genes among these 16 species. We then aligned all these ortholog genes using MACSE, a multiple sequence alignment software that aligns nucleotide sequences with respect to their amino-acid translation []. We set the options with a cost of 10 for frameshift and 60 for stop codo […]

call_split

Hyperendemic dengue transmission and identification of a locally evolved DENV 3 lineage, Papua New Guinea 2007 2010

2018
PLoS Negl Trop Dis
PMCID: 5849365
PMID: 29494580
DOI: 10.1371/journal.pntd.0006254
call_split See protocol

[…] bled against DENV reference genomes into contigs using CLC Genomics Workbench (Ver. 8.5.1). Complete assembled contigs were checked for chimeras and aligned against publicly available sequences using MACSE []. Alignments were verified in Se-Al 2.0 (http://tree.bio.ed.ac.uk/software/seal/) and analyzed using RAxML to generate a maximum-likelihood (ML) tree with ML bootstrap support based on the opt […]


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MACSE institution(s)
AGAP, Universite de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France; Institut des Sciences de l’Evolution de Montpellier (ISEM), UMR 5554, CNRS, EPHE, IRD, Universite de Montpellier, Montpellier, France
MACSE funding source(s)
Supported by the Agence Nationale de la Recherche “Investissements d’avenir/Bioinformatique” (ANR-10-BINF-01-02 project Ancestrome), Labex CeMEB “Centre Mediterraneen de l’Environnement et de la Biodiversite” (ANR-10-LABX-0004), and the European Research Council (ERC-2015-CoG-683257 project ConvergeAnt).

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