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CONTRAlign specifications


Unique identifier OMICS_30326
Name CONTRAlign
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes


  • person_outline Chuong Do
  • person_outline Serafim Batzoglou

Additional information


Unique identifier OMICS_30326
Name CONTRAlign
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 2.0.1
Stability Stable
Source code URL
Maintained Yes


No version available


  • person_outline Chuong Do
  • person_outline Serafim Batzoglou

Additional information

Publication for CONTRAlign

CONTRAlign citations


PnpProbs: a better multiple sequence alignment tool by better handling of guide trees

BMC Bioinformatics
PMCID: 5009527
PMID: 27585754
DOI: 10.1186/s12859-016-1121-7

[…] “”, we compare its performance with 13 leading multiple sequence alignment tools, including 10 using the progressive method: ClustalW [], Clustal Ω [], T-Coffee [], MAFFT [], MUSCLE [], ProbCons [], CONTRAlign [], Probalign [], MSAProbs [], GLProbs, and 3 using the non-progressive method: Align-m [], PicXAA [], and DIALIGN-PFAM []. PnpProbs’ performance is significant better, specially for distan […]


Generalized Centroid Estimators in Bioinformatics

PLoS One
PMCID: 3041832
PMID: 21365017
DOI: 10.1371/journal.pone.0016450

[…] : where is the initial probability of starting in state , is the transition probability from to and is the omission probability for either a single letter or aligner residue pair in the state .CONTRAlign (pair CRF) model : where is a parameter vector and is a vector of features that indicates the number of times each parameter appears, denotes the set of all possible alignments of and . […]


Predictions of RNA secondary structure by combining homologous sequence information

PMCID: 2687982
PMID: 19478007
DOI: 10.1093/bioinformatics/btp228
call_split See protocol

[…] , x′). We can obtain the probability distribution p(a)(θ|x, x′) on 𝒜(x, x′) by using the PHMM model (Durbin et al., ), the Miyazawa model (Miyazawa, ), the ProbAlign model (Roshan and Livesay, ), the CONTRAlign model (Do et al., ). By using the distributions, the alignment match probability p(a,x,x′)ik, which is the probability that xi is aligned with x′k, is computed as pik(a,x,x′) = p(a)(θik = 1 […]


Evidence for intelligent (algorithm) design

Genome Biol
PMCID: 1779572
PMID: 16879725
DOI: 10.1186/gb-2006-7-7-322

[…] h rather than of individual residues, they cannot easily be incorporated into standard methods based on hidden Markov models (HMMs) for sequence alignment without heuristics. The resulting algorithm, CONTRAlign (source code available online ), achieves the highest cross-validated pairwise protein alignment accuracies to date. […]


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CONTRAlign institution(s)
Stanford University, Stanford, CA, USA
CONTRAlign funding source(s)
Supported in part by NSF grant 0312459, by the NSF CAREER Award and the Alfred P. Sloan Fellowship.

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