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KaKs_Calculator 3. 0: Calculating Selective Pressure on Coding . . . - PubMed KaKs_Calculator 3 0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences Similar to the nonsynonymous synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as the ratio of non-coding nu …
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KaKs_Calculator 2. 0: A Toolkit Incorporating Gamma-Series Methods and . . . We present an integrated stand-alone software package named KaKs_Calculator 2 0 as an updated version It incorporates 17 methods for the calculation of nonsynonymous and synonymous substitution rates; among them, we added our modified versions of
Best Practices and Top Software for Calculating Ka Ks Ratios KaKs Calculator 2 0: Easy-to-use, supports multiple substitution models, and outputs statistical metrics HyPhy (Hypothesis Testing Using Phylogenies): Includes web-based tools like Datamonkey for streamlined analyses SeqinR (R Package): Facilitates integration with R pipelines for comprehensive analysis MEGA (Molecular Evolutionary Genetics
Ka Ks ratio - Wikipedia "KaKs_Calculator: calculating Ka and Ks through model selection and model averaging" Genomics, Proteomics Bioinformatics 4 (4): 259–263 doi: 10 1016 S1672-0229 (07)60007-2
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gKaKs: the pipeline for genome-level Ka Ks calculation Summary: gKaKs is a codon-based genome-level Ka Ks computation pipeline developed and based on programs from four widely used packages: BLAT, BLASTALL (including bl2seq, formatdb and fastacmd), PAML (including codeml and yn00) and KaKs_Calculator (including 10 substitution rate estimation methods) gKaKs can automatically detect and eliminate