Dear all, I would like to know if there is any statistical test / program that allows me check whether the third codon position in my alignment is evolving too fast (too divergent) that it should not be included in a phylogenetic analysis. I googled around and didn't get any hits. I appreciate if you can share what you know on this topic.
1 answer
There are a couple of tests for this, including Xia (2003, http://dx.doi.org/10.1016/S1055-7903(02)00326-3), which I gather is implemented in DAMBE.
Probably the most common way to asses this though, is to plot the number of 3rd codon substitutions in a sequence against some corrected distance . If the curve "plateaus" you know you are hitting saturation.
Log in to answer this question.
-
RepeatModeler contig size filter and parallelization
written by Anand Rao
-
Get chromosome sizes from fasta file
written by rioualen
-
Probing specific protein amino acid position changes in R
written by debra.ragland •
-
Genomic Annotation of Intervals (yes, again)
written by Tom
-
CNV calling with Control-FREEC? Significant calls
written by ivivek_ngs
-
What Does Elevation Of Dn/Ds Ratio Indicate?
written by qiyunzhu
-
What Does Samtools Flagstat Results Mean?
written by Sakti
-
Coments On This Feature: Alignment Coordinate Projection From 1.Bam To 2.Bam To Create 3.Bam?
written by 2184687-1231-83-
-
Fast Method To Detect Whether Snp Lies In Sequence Feature
written by Pi •
-
Deleting The 3Rd Codon Position In A Multiple Sequence Alignment And Substitution Saturation
written by Kartik Sunagar
I don't get it, if the third codon is highly divergent that is information per se, why would you throw it out ?
Because I fear (well, someone fears) that this could lead to bias in phylogenetic reconstruction.
Why are you studying nt seqs instead of aa seqs?
DNA provides more information, you know.
If you're studying really close lineages, like say strains of E. coli, then you're right. Otherwise, protein alignments almost certainly provide more information since things like saturation of the 3rd codon position can't happen there. For reference, see e.g. How To Tell If The Third Codon Position Is Saturated?.
You cannot just have "bias". Bias needs to be accompanied with a word like "it will bias towards [insert slant here]"
You may want to take a look at this post: How To Tell If The Third Codon Position Is Saturated?