More posts like this
-
What does it mean when dN/ds ratios are allowed to vary among branches?
written by Digsby •If dN/ds ratios are allowed to “vary among branches” (a common phrase in the literature), what does that acutally mean? It seems that dN/ds ratios …
-
Calculate dn ds ratio for the whole tree with python
written by Darrill •Hello, I'm using the codeml application with the python package ete3 in order to calculate the dN/dS ratio of my trees, but it appears that …
-
How can I interpret the results of a likelihood ratio test between substitution models?
written by Mimmi Ahlmén •I have estimated the dN/dS ratio with 3 different models: M0, M1a and M2a, this is an assignment, but I am having a hard time …
-
dN/dS within and between species
written by krc3004 •Hi all, Recently I have been very interested in calculating the dN/dS ratio to estimate rates of nonsynonymous and synonymous substitutions. Since I've just started …
-
Should I average dN/dS over all CDS for a gene or consider only the longest transcript?
written by shreyasibiswas88 •Hi everyone, I have calculated dN/dS ratio for ALL transcripts for ALL genes for my study systems (different species of rats) using codeml in PAML. …
-
Is there any tool to calculate dn/ds for orthologues?
written by ThulasiSHi all I am trying to calculate dn/ds ratio for several genes. I am trying to analyze the selection pressure on several bacterial genes. I …
-
How can I calculate p value for rate analysis of particular lineage?
written by evo_genomics •How can I calculate p value for rate analysis of particular lineage? I have used Mega 6 for estimation of dN/dS ratio? Kindly guide me. …
-
calculate the number of Non-Synomous and Synonymous SNP sites
written by upendrakumar.devisettyHi, I have a VCF containing the SNP information between the two genotypes of interest and using that VCF and i have annotated the SNPs …
-
What Does Elevation Of Dn/Ds Ratio Indicate?
written by qiyunzhu<p>Hello folks,</p> <p>I am writing a paragraph regarding a gene family, in which <strong>a specific clade has increased dN/dS ratio comparing to other clades</strong>. I …
-
Dn/Ds Ratio - Paml : How Is It Possible To Obtain Negative Values For Dn Or Ds ?
written by Francois Olivier Hébert •<p>Hi,</p> <p>I have a set of 383 coding sequences in which there is a whole bunch of SNPs. I only have two species (2 populations …