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MergeAlign specifications


Unique identifier OMICS_10430
Name MergeAlign
Interface Web user interface
Restrictions to use None
Input data Unaligned protein sequences in FASTA format or aligned protein, DNA or RNA sequences in FASTA or CLUSTAL format
Programming languages Python
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Steven Kelly

Publication for MergeAlign

MergeAlign citations


Unifying the global phylogeny and environmental distribution of ammonia oxidising archaea based on amoA genes

Nat Commun
PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] nments were selected after evaluation with MUMSA based on multiple overlap (MOS) and average overlap (AOS) scores. Alignments with MOS above the average of the 10 alignments selected were merged with MergeAlign, and columns not supported by at least two independent alignments, or containing >80% gaps, were excluded. The consensus alignment was based on PSI-Coffee, MSAProbs, G-INS-i, E-INS-i and L- […]


Genetic Regulation of the 2D to 3D Growth Transition in the Moss Physcomitrella patens

Curr Biol
PMCID: 5807088
PMID: 29395927
DOI: 10.1016/j.cub.2017.12.052

[…] version 10 were subject to orthogroup inference using OrthoFinder []. The orthogroup containing the NOG1 gene was identified and the constituent sequences subject to multiple sequence alignment using MergeAlign []. It was apparent from manual inspection of the multiple sequence alignment that several gene models were likely incorrect (Spirodella polyriza, Vitis vinifera, Eucalyptus gradis, Setaria […]


An Alternative Strategy for Trypanosome Survival in the Mammalian Bloodstream Revealed through Genome and Transcriptome Analysis of the Ubiquitous Bovine Parasite Trypanosoma (Megatrypanum) theileri

Genome Biol Evol
PMCID: 5737535
PMID: 28903536
DOI: 10.1093/gbe/evx152

[…] Orthologous gene groups containing only single copy genes in all species were selected for inclusion in the phylogenetic analysis. The individual orthologous groups were aligned using MergeAlign () and edited to remove all gap-containing columns and columns containing fewer than two character states. MergeAlign was selected as it has previously been shown to increase topological co […]


Lineage specific proteins essential for endocytosis in trypanosomes

PMCID: 5399782
PMID: 28232524
DOI: 10.1242/jcs.191478

[…] pred), hmmscan ( and InterProScan ( For phylogenetic reconstruction, sequences were aligned using MergeAlign () and edited for gaps and low conservation. The correct evolutionary model was assessed using ProtTest ( and phylogenetic trees were c […]


Nonreciprocal complementation of KNOX gene function in land plants

New Phytol
PMCID: 5637896
PMID: 27886385
DOI: 10.1111/nph.14318
call_split See protocol

[…] the MEINOX, ELK and TALE‐HD domains as a guide. The amino acids were then translated back to their corresponding codon sequences using a custom Perl script. BELL protein alignment was obtained using MergeAlign (Collingridge & Kelly, ) with default parameters. The aligned sequences were then edited and trimmed manually to conserve homologous sites only (Fig. S1; Notes S5, S6). Maximum‐likelihood t […]


Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms

Genome Biol
PMCID: 5109750
PMID: 27842572
DOI: 10.1186/s13059-016-1087-9

[…] e copy gene orthogroups were further filtered to retain those that had representation from at least three species per group (LN, MN and HN). Protein sequences for these orthogroups were aligned using MergeAlign []. The corresponding coding sequences were re-threaded back through the aligned amino acid sequences using custom Perl scripts. These multiple sequence alignments were then filtered so tha […]


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MergeAlign institution(s)
Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, Devon, UK; Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, UK

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