TranslatorX protocols

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TranslatorX specifications

Information


Unique identifier OMICS_22371
Name TranslatorX
Interface Web user interface
Restrictions to use None
Input data Some nucleotide sequences, protein alignment, genetic code or alignment cleaning.
Computer skills Basic
Version 0.9
Stability Stable
Maintained No

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Information


Unique identifier OMICS_22371
Name TranslatorX
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained No

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Publication for TranslatorX

TranslatorX in pipelines

 (5)
2016
PMCID: 4945904
PMID: 27417983
DOI: 10.1038/srep29690

[…] genes (pcgs) were first extracted using purpose-built perl scripts based on annotations and then separately aligned according to their corresponding amino acid translations using the software translatorx. the gaps were not removed as they are known to contain valuable information for phylogenetic analyses. the concatenated nucleotide sequence alignment from 13 pcgs (total = 11,433 bp) […]

2016
PMCID: 4989294
PMID: 27538950
DOI: 10.1186/s12862-016-0729-6

[…] used to assess the of clade-specific gal-8 evolution by quantifying the rate of non-synonymous substitutions of lgals8 []. guided by the amino acid alignment, the codons of the genes were aligned in translatorx []. the free ratios model was used to calculate the maximum likelihood estimate of non-synonymous substitution (dn) for each branch of the given tree. the null model assumes […]

2015
PMCID: 4507762
PMID: 25979997
DOI: 10.1093/jxb/erv220

[…] gene pairs., blastp analysis for the arabidopsis cds and its homologues as well as radish orthologue candidates was carried out. alignments of assembled nucleotide sequences were conducted using translatorx, an online tool that aligns nucleotide sequences based on the translated amino acid sequences (). poorly aligned regions were removed from tree analysis either manually or using default […]

2015
PMCID: 4563886
PMID: 26353816
DOI: 10.1186/s13059-015-0754-6

[…] the loess function in ggplot2 was used to draw the curve., we used the coding sequences of non-syntenic genes and their best blastp hit in brachypodium distachyon to make an alignment with translatorx [] for calculating ka and ks. rates were calculated by the nei and gojobori method using codeml (part of the paml package; []). this resulted in ka and ks rates for 3,962 pairs […]


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TranslatorX in publications

 (123)
PMCID: 5920176
PMID: 29700141
DOI: 10.1128/genomeA.00240-18

[…] proteins (l1 and l2), and a noncoding control region., seventy-six pv l1 nucleotide sequences were retrieved from the papillomavirus episteme resource (http://pave.niaid.nih.gov/) and aligned in translatorx () guided by amino acid translations with the muscle alignment option. maximum likelihood phylogenetic analysis performed in iq-tree () supported the bottlenose dolphin papillomavirus […]

PMCID: 5915565
PMID: 29720990
DOI: 10.3389/fpls.2018.00504

[…] for 40 min at 4°c and the thermolysin was inactivated with ib with 14 mm edta. sds–page and fluorography was used to analyze the samples., multiple sequence alignments (msas) were generated with the translatorx server () using mafft v.7 software () and curated in jalview v.2.8.0 or gblocks [standard parameters; (; )] for large amount of data. msas were visualized in jalview v.2.8.0 () […]

PMCID: 5897359
PMID: 29651164
DOI: 10.1038/s41598-018-24301-6

[…] were calculated using the shimodaira-hasegawa method., the corresponding protein sequences that composed the og were aligned with mafft v7 and a codon alignment for each og was then created with translatorx using the nucleotide cds sequence and aligned protein data as a guide. maxalign v1.1 was used in codon mode to remove poorly aligned sites and sequences. any taxa removed from the og […]

PMCID: 5888179
PMID: 29635329
DOI: 10.1093/gbe/evy063

[…] numbers ky0819063–ky0819066, and ky0819068. the sequence of bryopsis hypnoides (nc_013359) was reannotated following ., alignments of named chloroplast protein-coding genes were inferred using translatorx (), which translates sequences to amino acids, uses mafft () to align the amino acid sequences and generates the corresponding nucleotide alignments. individual gene alignments […]

PMCID: 5841385
PMID: 29608721
DOI: 10.1093/gbe/evy046

[…] study the glutamine codon usage in the orthologs, we followed the same procedure, counting the number of caa and cag triplets forming the q stretches. in this case, we used the standalone version of translatorx (), with default parameters, to easily visualize the nucleotide alignments separated by codons., the length of a q stretch was considered to be stable if at least half of the orthologs […]


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TranslatorX institution(s)
Departamento de Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales, Madrid, Spain; Department of Genetics, Evolution and Environment, University College London, London UK

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