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• Error in Calculation of Ka/Ks value using Ka/Ks calculator
  Hi, I am using Ka/Ks calculator software for identification of rapidly evolving genes. I ali...
• sequence input for doing ka/ks analysis
  Hello could anybody help me to put the sequence for doing ka/ks analysis? which sequence to put ...
• Most suitable alignment program for Ka/Ks analysis of whole genome coding sequences
  Hi, I've been trying to get Ka/Ks scores of genome-wide pairwise alignments of coding sequences ...
• Ka/Ks (Or Dn/Ds) Calculation From Sequenced Transcriptome Contigs
  I have around 25,000 contigs each for two species. I'm trying to calculate Ka and Ks (or Dn and D...
• Pre-calculated Ka/Ks ratio per gene of human genome
  Hi there, I was wondering if there is somewhere a list of pre calculated Ka/Ks ratio's for all h...
• calculate Ka Ks from SNP table
  Dear all, I have two subset with their inter-subset SNP comparison as below ![enter image descr...
• How many sequences for Ka/Ks Ratio
  Hello, I wish to calculate Ka/Ks Ratio and test for selection with Mega. I have several sequence...
• Aligning genome wide coding sequences of two species for Ka/Ks calculation
  Hi, I have two fasta files each containing ~300,000 sequences of coding exons for one species. B...
• Comparing diversity between two paralogs using a VCF file
  I'm looking at two homeologs and trying to gain information about their potentially different evo...
• How to Calculate Non-Synonymous Changes Between Proteins?
  I know that Ka/Ks ratio is very relevant to what I'm looking for, but as far as I know, the tools...
• How to know synonymous and non-synonymous SNPs from transcriptome sequencing
  I obtained a SNP list (VCF format) from a sample's transcriptome (assembled by Trinity). ORFs wer...
• Tool to estemate Ka/Ks using variant calling data?
  Hi, I'm in the process of comparing RNA-seq data from two fungal isolates by aligning against a ...
• how to use Ka/Ks calculator
  Hi, I want to calculate the divergence time of genes. Can somebody guide me on how to use the KaK...
• Statistical tests for Ka/Ks (dn/ds) ratio?
  I have been using MEGA to calculate the Ka/Ks for genes between 5 species. Is there a statistical...
• how to normalise/Scale the FPKM and Ka/Ks value in a matrix?
  I've got two columns about RNA-seq FPKM between two species and a ka/ks column of these ortholog,...
• How to retrieve single Ka and Ks values from a whole multiple sequence alignment using PAML (codeml)?
  I am able to retrieve ka/ks ratio for a multiple sequence alignment using the model=0 and NSsites...
• Calculating the number of synonymous and non-synonymous sites for genes
  Hi all, I have a list of the numbers of synonymous and non-synonymous SNPs for a large set of ge...
• KaKs_calculator doesn't work with sequences
  Hi! Question about KaKs_Calculator2.0 I would like to calculate Ka/Ks for the sequences below. ...
• Is there a database with calculated Ka/Ks ratios for human/mouse genomes?
  The header pretty much sums up my question. I need (somehow calculated) Ka/Ks ratios for human/mo...
• How to perform KaKs_Calculator from SNPEff's output
  Hi, all, I have obtained the annotated SNP (VCF file) by SNPEff. How to calculate ka/ks using Ka...
• How To Calculate The Number Of Potential Synonymous And Nonsynonynous Sites
  Hi everyone, Does anyone know how to calculate the number of synonymous sites for a certain sequ...