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MACAW specifications


Unique identifier OMICS_15829
Alternative name Multiple Alignment Construction & Analysis Workbench
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS, Windows
Computer skills Medium
Version 2.05
Stability Stable
Maintained Yes


No version available

Publication for Multiple Alignment Construction & Analysis Workbench

MACAW citations


Recurrent rearrangements of the Myb/SANT like DNA binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma

PLoS One
PMCID: 5315303
PMID: 28212443
DOI: 10.1371/journal.pone.0171265
call_split See protocol

[…] ins within MSANTD3 were identified by search of NCBI’s conserved domain database []. Local protein sequence alignments were performed using the Multiple Alignment Construction and Analysis Workbench (MACAW) []. Global protein sequence-alignments were performed using ClustalX []. A boot-strapped phylogenetic tree was displayed with TreeView []. […]


Evolution of the Land Plant Exocyst Complexes

Front Plant Sci
PMCID: 3399122
PMID: 22826714
DOI: 10.3389/fpls.2012.00159
call_split See protocol

[…] For initial estimation of sequence similarity and detection of possible problems with gene structure prediction (i.e., missing or extraneous exons), the interactive MACAW tool (Schuler et al., ; Lawrence et al., ), or the automated tools ClustalX (Thompson et al., ) and KALIGN (Lassmann and Sonnhammer, ) have been employed to generate preliminary versions of mult […]


Activity, specificity and structure of I Bth0305I: a representative of a new homing endonuclease family

Nucleic Acids Res
PMCID: 3239194
PMID: 21890897
DOI: 10.1093/nar/gkr669
call_split See protocol

[…] identified in the NCBI sequence databases and JCVI data using BLAST sequence searches and BLIMPS motif searches as previously described (). Multiple sequence alignments were constructed with MEME (), MACAW (), DIALIGN-TX () and GLAM-2 () programs.RecA gene regions corresponding to the I-Bth0305I cleavage and intron insertion site were identified by searching complete genomes of bacteria from the N […]


Domain annotation of trimeric autotransporter adhesins—daTAA

PMCID: 2373917
PMID: 18397894
DOI: 10.1093/bioinformatics/btn118
call_split See protocol

[…] t et al., ) using HHPred (Soding, ) on the Protein Data Bank filtered at 70% sequence identity (pdb70). Sequences were extracted using the Entrez service ( and aligned in MACAW (Schuler et al., ) and MUSCLE (Edgar, ). Domain boundaries were defined iteratively by sequence conservation and context. Coiled-coils were predicted using COILS (Lupas et al., ) and Marcoil (De […]


The prokaryotic antecedents of the ubiquitin signaling system and the early evolution of ubiquitin like β grasp domains

Genome Biol
PMCID: 1779556
PMID: 16859499
DOI: 10.1186/gb-2006-7-7-r60

[…] LAST.Multiple alignments were constructed using the T_Coffee, MUSCLE, and PCMA programs followed by manual adjustments based on PSI-BLAST results [-]. The GIBSS sampling method, as implemented in the MACAW program, was used for the identification and statistical evaluation of conserved motifs in multiple protein sequences [,]. All large-scale sequence analysis procedures were carried out using the […]


Multiple sequence alignment with user defined anchor points

Algo Mol Biol
PMCID: 1481597
PMID: 16722533
DOI: 10.1186/1748-7188-1-6

[…] method that would accept such user-defined homology information and would then align the remainder of the sequences automatically, respecting these user-specified constraints.The interactive program MACAW [] can be used for semi-automatic alignment with user-defined constraints; similarly the program OWEN [,] accepts anchor points for pairwise alignment. Multiple-alignment methods accepting pre-d […]


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MACAW institution(s)
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

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