DIALIGN-TX statistics

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DIALIGN-TX specifications

Information


Unique identifier OMICS_24606
Name DIALIGN-TX
Alternative name DIALIGN-T
Interface Web user interface
Restrictions to use None
Input data A file containing protein sequences or a file containing DNA sequences.
Input format Multiple FASTA
Computer skills Basic
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/DIALIGN-TX

Maintainers


  • person_outline Burkhard Morgenstern <>
  • person_outline Amarendran Subramanian <>

Information


Unique identifier OMICS_24606
Name DIALIGN-TX
Alternative name DIALIGN-T
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.0.2
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/DIALIGN-TX

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Maintainers


  • person_outline Burkhard Morgenstern <>
  • person_outline Amarendran Subramanian <>

Publications for DIALIGN-TX

DIALIGN-TX in pipelines

 (2)
2016
PMCID: 5057483
PMID: 27777508
DOI: 10.1186/s41182-016-0032-7

[…] using the primers designed from the sequence previously reported []., phylogenetic analyses of the vp region of selected tick-borne orbivirus proteins and amino acid sequences were aligned using the dialign-tx v1.0.2 and trimal v1.2 [–]. the substitution models were determined by prottest v3.4.1 while the phylogenetic trees were reconstructed by the maximum likelihood model using phyml v3.0.1 [, […]

2006
PMCID: 1434745
PMID: 16448571
DOI: 10.1186/1471-2164-7-18

[…] stop codons (from eight sequences with one to three internal stops each) were changed to amino acid ambiguities ("x")., alignment of amino acid kinesin-motor-domain sequences was performed using dialign-t 0.1.2 [] with the default settings (length of a low-scoring region = 4; maximum fragment length that is allowed to contain regions of low quality = 40). amino acids from individual […]


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DIALIGN-TX in publications

 (29)
PMCID: 5904100
PMID: 29666365
DOI: 10.1038/s41467-018-03861-1

[…] aligned with 14 different methods: l-ins-i, e-ins-i and g-ins-i strategies of mafft v7; psi-coffee, expresso; t-coffee; probcons v1.12; probalign v1.3; prank; muscle v3.7; msaprobs v0.9.7; kalign; dialign-tx; and clustal omega. the 10 best alignments were selected after evaluation with mumsa based on multiple overlap (mos) and average overlap (aos) scores. alignments with mos above the average […]

PMCID: 4799563
PMID: 26992851
DOI: 10.1186/s12859-016-0945-5

[…] standard for a long time. then, it was followed by the “next generation” of aligners, such as t-coffee [], mafft [–], muscle [, ], probcons [], prank [, ], mummals [], probalign [], m-coffee [] and dialign-tx [], which feature improved computational speed and/or accuracy, and currently they and the upgraded clustalw can be regarded as the state-of-the-art programs to search for an optimum msa. […]

PMCID: 4780264
PMID: 26840490
DOI: 10.1038/nature16941

[…] used a more accurate phylogenetic approach. we used a similar pipeline to that described in. in brief, multiple sequence alignments using three different aligners, muscle v3.8.31, mafft v6.861b and dialign-tx 1.0.2, were performed in forward and reverse orientation. the six resulting alignments were combined with m-coffee v8.80 into a maximal-consensus alignment, which was trimmed using trimal […]

PMCID: 4267518
PMID: 25574120
DOI: 10.4137/EBO.S19199

[…] comparison of 10 most popular multiple sequence alignment (msa) tools, namely, muscle, mafft(l-ins-i), mafft (fft-ns-2), t-coffee, probcons, sate, clustal omega, kalign, multalin, and dialign-tx is presented. we also focused on the significance of some implementations embedded in algorithm of each tool. based on 10 simulated trees of different number of taxa generated by r, 400 […]

PMCID: 4015676
PMID: 24602402
DOI: 10.1186/1748-7188-9-4

[…] accuracy and computational cost has become a critical indicator of the most suitable msa program. we compared both accuracy and cost of nine popular msa programs, namely clustalw, clustal omega, dialign-tx, mafft, muscle, poa, probalign, probcons and t-coffee, against the benchmark alignment dataset balibase and discuss the relevance of some implementations embedded in each program’s […]


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DIALIGN-TX institution(s)
Wilhelm-Schickard-Institut fur Informatik, University of Tubingen, Tubingen, Germany; Institute of Microbiology and Genetics, University of Gottingen, Gottingen, Germany; Department of Mathematics, Indian Institute of Technology, Kharagpur, India
DIALIGN-TX funding source(s)
Supported by Deutsche Forschungsgemeinschaft (grants MO 1048/1-1 and MO 1048/6-1, in part).

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