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MCALIGN specifications

Information


Unique identifier OMICS_03699
Name MCALIGN
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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Maintainers


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

Publications for MCALIGN

MCALIGN in pipelines

 (3)
2010
PMCID: 2997565
PMID: 21068212
DOI: 10.1093/gbe/evq066

[…] strictu saccharomyces species, the average percent identity was close to 40% and not significantly different from that of randomized intergenic regions. we also calculated percent identity from mcalign2 alignments using insertion, deletion, and substitution parameters derived from closely related strains of s. cerevisiae (see materials and methods). mcalign2 alignments showed lower percent […]

2007
PMCID: 1865379
PMID: 17451608
DOI: 10.1186/1471-2148-7-66

[…] ambiguity bordering indels, we generated a second alignment set for the intergenic data, eliminating eight bases on either side of each indel. we also aligned all intergenic sequences using mcalign2, a program specifically for alignments of intergenic sequences containing indels []. this program is optimized for drosophila indel patterns, and parameters for arabidopsis deletions […]

2007
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 []. to infer an appropriate indel frequency model, we first aligned the dataset with an indel model […]


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MCALIGN in publications

 (9)
PMCID: 4006747
PMID: 24784238
DOI: 10.1371/journal.pntd.0002839

[…] (cds) or non-coding (igr) regions, as described below., alignment of coding sequences was done using muscle , . however, to align igr regions, which contain more gaps and polymorphims, we used the mcalign algorithm , , that explicitly models indels based on prior information. to generate this prior information, we first aligned igr regions using sigma , , which is designed specifically […]

PMCID: 2997565
PMID: 21068212
DOI: 10.1093/gbe/evq066

[…] were included in the alignments, and percent identity was calculated using intergenic regions defined in s. cerevisiae. a gap open penalty of 6 and a gap extension penalty of 0.2 were used. mcalign2 () was also used to generate pairwise alignments. a custom insertion/deletion rate was used based on data from three closely related s. cerevisiae strains (). the relative rate of point […]

PMCID: 2766791
PMID: 20190955
DOI: 10.2174/138920209789177575

[…] of the individual alignment regions. it was demonstrated that using geometrically distributed indel lengths based on pair-hmms has many potential advantages []. more recently, another method called mcalign2 [] also adopted pair-hmms with a slightly different structure, for global pairwise alignment of noncoding dna segements. using pair-hmms to describe specific indel length distributions […]

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

[…] (gaps) between the pair of sequences []. a solution to this problem is to compute probabilities of alternative alignments according to explicit models of indel evolution. based on this method, mcalign2 has been developed to tackle the problem of aligning noncoding dna []., selective constraints of introns have recently been investigated in drosophila, mammals and other animals [-,]. […]

PMCID: 1865379
PMID: 17451608
DOI: 10.1186/1471-2148-7-66

[…] ambiguity bordering indels, we generated a second alignment set for the intergenic data, eliminating eight bases on either side of each indel. we also aligned all intergenic sequences using mcalign2, a program specifically for alignments of intergenic sequences containing indels []. this program is optimized for drosophila indel patterns, and parameters for arabidopsis deletions […]


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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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