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ParaAT specifications


Unique identifier OMICS_29580
Name ParaAT
Alternative name Parallel Alignment & back-Translation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Source code URL
Maintained Yes




No version available



  • person_outline Zhang Zhang
  • person_outline Lin Dai

Publication for Parallel Alignment & back-Translation

ParaAT citations


Evolutionary Origin, Gradual Accumulation and Functional Divergence of Heat Shock Factor Gene Family with Plant Evolution

Front Plant Sci
PMCID: 5801592
PMID: 29456547
DOI: 10.3389/fpls.2018.00071

[…] The protein sequence alignments and the relative cDNA sequences were converted into corresponding codon alignments by using the paraAT 2.0 program (Zhang et al., ). The nonsynonymous (Ka) and synonymous (Ks) rates (Ka/Ks) of each codon alignment in the paired sequences were calculated by using KaKs_Calculator 2.0 (Wang et al., […]


Genomic structure and evolution of the mating type locus in the green seaweed Ulva partita

Sci Rep
PMCID: 5601483
PMID: 28916791
DOI: 10.1038/s41598-017-11677-0

[…] e was identified. After manual checking, two gametologs were found to contain no CDSs that could form pairs with their counterparts. Pairs of CDSs for the individual gametologs were aligned using the ParaAT package, and the alignments obtained were used to calculate the synonymous and non-synonymous substitution rates using the maximum-likelihood and approximation methods with nucleotide substitut […]


Genome wide Analysis and Expression Divergence of the Trihelix family in Brassica Rapa: Insight into the Evolutionary Patterns in Plants

Sci Rep
PMCID: 5526864
PMID: 28743951
DOI: 10.1038/s41598-017-06935-0

[…] duplicated pairs of trihelix genes were aligned using ClustalW2. We calculated the synonymous rate (Ks), non-synonymous rate (Ka), and evolutionary constraint (Ka/Ks).An in-house Perl script based on ParaAT54 was used to translate the protein alignments into coding sequence alignments and based on that we calculated the Ka (nonsynonymous substitution rate) and Ks (synonymous substitution rate) val […]


The mitochondrial genomes of the acoelomorph worms Paratomella rubra, Isodiametra pulchra and Archaphanostoma ylvae

Sci Rep
PMCID: 5431833
PMID: 28500313
DOI: 10.1038/s41598-017-01608-4
call_split See protocol

[…] tween a 9.7 kb section of the P. rubra mitochondrial genome originating from worms sampled in Filey, Yorkshire (UK) and Barcelona (Spain). For eight protein-coding genes found on this section we used ParaAT (v2.0) to calculate translation alignments and the KaKs calculator (v1.2) to access substitution rates. Also using Geneious we calculated a difference matrix for the cox1 barcoding gene of the […]


Adaptation and evolution of deep sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow water species

Sci Rep
PMCID: 5387418
PMID: 28397791
DOI: 10.1038/srep46205

[…] alysis and aligned sequences with less than 50 amino acids were excluded. Only 1:1 orthologous genes were used for base substitution analysis. The input files for Ka/Ks_Calculator were prepared using ParaAT1.0. A maximum likelihood method with the MLPB model was used to calculate non-synonymous substitutions per nonsynonymous site (Ka), synonymous substitutions per synonymous site (Ks), and the ra […]


Genomic analyses of the ancestral Manila family of Mycobacterium tuberculosis

PLoS One
PMCID: 5386241
PMID: 28394899
DOI: 10.1371/journal.pone.0175330

[…] SNPs were also identified using MUMer 3 package []. Synonymous substitution rate (Ks) and the ratio of nonsynonymous substitution rate to synonymous substitution rate (Ka/Ks ratio) were calculated by ParaAT and KaKs_Calculator packages [, ]. Density plots of Ka/Ks and Ks values were created using R commands and heat scatter plots of Ka and Ks values were generated by LSD package []. […]


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ParaAT institution(s)
CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China; School of Mathematics and Computer Science, Ningxia University, Yinchuan, Ningxia, China; School of Computer Science and Technology, Beijing Institute of Technology, Beijing, China
ParaAT funding source(s)
Supported by the ‘‘100-Talent Program’’ of Chinese Academy of Sciences (Y1SLXb1365), National Programs for High Technology Research and Development (863 Program; Grant No. 2012AA020409), the Ministry of Science and Technology of the People’s Republic of China, and National Natural Science Foundation of China (60803050, 61132009).

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