2024 Tbtools simple ka/ks calculator

Tbtools simple ka/ks calculator

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August undefined, 2024

WebFeb 14, 2024 · The duplication pattern of the AhR2R3-MYB genes was visualized by the Amazing Super Circos package of TBtools. The Ka/Ks value was completed by the Simple Ka/Ks Calculator program of TBtools. Duplication time was calculated by the following formula as described by Bertioli et al. (2016): T = Ks/2λ (λ = 8.12 × 10 −9). WebSep 15, 2024 · Chen/TBtools, access time: 20 July 2024) using Amazing Gene Location. T o exhibit the. ... Simple Ka/Ks Calculator software [73]. Int. J. Mol. Sci. 2024, 22, 9957 18 of 22. 4.4. Analysis of the ...

Genome-wide analysis of R2R3-MYB genes in cultivated peanut

WebApr 14, 2024 · Synteny analysis on internal CHR genes in soybean was conducted with One Step MCScanX plugin in TBtools, and visualization was performed with Advanced Circos plugin . Nonsynonymous (Ka) and synonymous (Ks) substitution rates for each Snf2 gene pair were calculated with Simple Ka/Ks Calculator in TBtools . WebMar 9, 2024 · Here, we present TBtools (a T oolkit for B iologists integrating various biological data handling tools ), a stand-alone software with a user-friendly interface. The toolkit incorporates over 100 ... quickbooks pro 2018 download intuit

Genome-wide identification and characterization of the

WebAug 26, 2024 · Synonymous (Ks) and nonsynonymous (Ka) substitution rates were calculated using the Simple Ka/Ks Calculator (NG) in TBtools. The patterns of selection were detected on the basis of the Ka/Ks ratio between paralogs. 2.6. Cis-Acting Regulatory Elements (CAREs) Analysis. WebI determined the Ka/Ks ratio for the matK gene. The MAFFT alignment showed 6 SNPs which were non-synonyms and covert six amino acid. The whole size of the matK gene … WebThe value of Ka and Ks were calculated by “simple Ka/Ks_calculation” in TBtools, and the formula T = Ks/r was used to calculate the divergence time . 4.3. Alignment and Phylogenetic Analysis. Multiple alignment of selected full-length amino acid sequences was aligned with default parameters using MAFFT v7 . quickbooks pro 2019 product number

Genome-wide identification, classification and expression …

Tbtools simple ka/ks calculator

IJMS Free Full-Text Genome-Wide Identification of the AGC …

WebJul 9, 2014 · This software is a toolkit of incorporating gamma series methods and sliding window strategies. Please cite the selected following reference when using the … WebOct 7, 2024 · TBtools基因家族分析详细教程 (3)基因家族成员的进化分析1. 包括 1多序列比对与可视化 Mega（Muscle）进行序列比对，JalView进行多序列比对结果的可视化 2进化 …

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WebSep 20, 2024 · The duplication types and collinear blocks were discovered and were analyzed using One Step MCScanX and Simple Ka/Ks calculator (NJ) of Tbtools, and a diagram of gene duplication events was drawn using the Tbtools. ... The Ka/Ks for segmental duplication was 0.05–1.21 with an average of 0.31, while the ratio of tandem … WebApr 7, 2024 · In addition, TBtools with a simple Ka/Ks(S2) calculator were applied to calculate Ka/Ks values between gene pairs. 2.5. Conserved Motifs and Gene Structure Prediction of the PAL Gene Family in Chinese Cabbage. The gff3 annotation file of Chinese cabbage was downloaded from the Brassica database ...

WebApr 3, 2024 · Information on the chromosomal location of ChDof genes was obtained from the C. humilis genome annotation files, and the distribution of ChDof genes on C. humilis chromosomes, according to the Poisson model, was determined using TBtools. The Simple Ka/Ks Calculator (NG) tool of TBtools was used to calculate the Ka, Ks, and Ka/Ks … WebDec 30, 2024 · The nonsynonymous substitution ratios (Ka), synonymous substitution ratios (Ks), and Ka/Ks ratios of the PgrAQP family genes were calculated using the TBtools …

WebAbout Press Copyright Contact us Creators Advertise Developers Terms Privacy Policy & Safety How YouTube works Test new features NFL Sunday Ticket Press Copyright ... WebDec 16, 2024 · The Ka/Ks ratio of 12 homologous genes was less than 1, which indicated that the PtDi19 gene family of poplar has experienced a strong purification selection pressure during its evolution. ... (Ka) and the synonymous substitution rate (Ks) of these homologous gene pairs were calculated with the simple Ka/Ks calculator in TBtools …

WebAug 6, 2024 · The “Simple Ka/Ks Calculator (NG)” function in TBtools (v1.09876) was used to calculate Ka, Ks, and Ka/Ks values. 4.3. Transcriptome Analysis, GCNA, and WGCNA of Brassicaceae Hormone-Related TFs.

WebMar 5, 2024 · The Simple Ka/Ks Calculator (NG) of TBtools was used to calculate the nonsynonymous (Ka) and synonymous (Ks) substitution values and the Ka/Ks values of … quickbooks pro 2018 download linkWebOct 19, 2024 · The simple Ka/Ks calculator tool of TBtools was applied to calculate Ka, Ks and Ka/Ks ratios of duplicated genes. Divergence time (T) is calculated by the equation T = Ks/(2 × 9.1 × 10 −9) × 10 −6 million years ago (Mya) . 4.4. gcHap Analysis of the AGC Genes in 3KRG. ship store captiva islandWebSep 13, 2024 · The ratios of synonymous (Ks) and non-synonymous (Ka) nucleotide substitutions (Ka/Ks) between homologous gene pairs were also calculated via Simple Ka/Ks Calculator module in TBtools . Additionally, the divergence time was calculated using the formula T = Ks/2r. ship store darwinWebJun 21, 2024 · The diagram was generated by TBtools . The nonsynonymous (Ka) and synonymous (Ks) substitution ratios were calculated by Simple Ka/Ks Caculator in … quickbooks pro 2016 license keyWebNov 15, 2024 · The Ka/Ks values of 6 pairs of AAT orthologous genes between allotetraploid G. barbadense L. and diploid G. raimondii L. were greater than one, accounting for 3.53% of them (6/170), the Ka/Ks values of two pairs of them were great than 2, accounting for 1.18% of them (2/170), and the Ka/Ks values of the rest of them were in the range of 0 and 0.95. quickbooks pro 2020 tool hubWebJun 1, 2024 · In addition, TBtools with a simple Ka/Ks(S2) calculator were applied to calculate Ka/Ks values between gene pairs. ... Identification of PAL Gene in Purple … quickbooks pro 2021 cdwWebJun 3, 2024 · The values of Ka and Ks were calculated with the Simple Ka/Ks Calculator (NG) in TBtools software. Generally, Ka/Ks < 1.0 indicates purifying or negative selection, Ka/Ks = 1.0 denotes neutral selection, and Ka/Ks … shipstore kiel canal gmbh