Question: How to find historical variations in mutation rate in an epidemic
1
gravatar for jaynaythan
3.0 years ago by
jaynaythan10
jaynaythan10 wrote:

Historical variations in mutation rate in an epidemic ...

mlst.warwick.ac.uk/mlst/AGroup/team/markPDF/71pdf

The genetic diversity of Yersinia pestis, the etiologic agent of plague, ...... the software PHYML with the HKY model (11), and 500 bootstrap replications.

Download Appendix (PDF) www.pnas.org/content/suppl/2012/12/26/1205750110.../sapp.pdf 26 Dec 2012 - of 500 bp. ... the software PHYML with the HKY model (11), and 500 bootstrap replications. .... (2009) Draft genome sequences of Yersinia pestis isolates from .... The tree was constructed using PHYML with 500 bootstrap ...

Two-Step Source Tracing Strategy of Yersinia pestis and Its ... www.ncbi.nlm.nih.gov › NCBI › Literature › PubMed Central (PMC) by Y Yan - ‎2014 - ‎Cited by 9 - ‎Related articles 9 Jan 2014 - Here, we employed Yersinia pestis genomes from a plague outbreak .... time to reconstruct the MLTree with 1,000 bootstrap iterations (the first step) ... size of 500 bp for each isolate according to the manufacturer's instructions. A Phylogenomic Study of Endosymbiotic Bacteria mbe.oxfordjournals.org/content/21/6/1110.full.pdf by B Canbäck - ‎2004 - ‎Cited by 75 - ‎Related articles distances and 500 bootstrap replicates by using PAUP* version 4.0b10 for ... PAUP* by using only one repetition in the heuristic search. For the ... Yersinia pestis.

dna • 846 views
ADD COMMENTlink modified 3.0 years ago by Istvan Albert ♦♦ 80k • written 3.0 years ago by jaynaythan10

Can you tell us how the phylogenetic tree was created? Are you using a reference genome and the aligning all strains to it?

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax65k

It was aligned to a random genome in the list. Using the "-r !"Parsnp command

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by jaynaythan10

What program are you using for this? In the past I have always worked with individual genes when creating phylogenies.

ADD REPLYlink written 3.0 years ago by genomax65k

Raxml. this is core genome alignment

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by jaynaythan10

What do you mean by "core genome alignment"? An old post on biostars questions ability of raxml to do whole genome phylogenies: Phylogenetic Analysis Of Whole Genomes Perhaps someone else may have additional suggestions.
The possibility of samples being mislabeled (during submission or prior) is there.

You may find this paper interesting.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax65k

One would hope things have progressed in 5 years since that post!

ADD REPLYlink written 3.0 years ago by jaynaythan10

I would recommend spending some time formatting your question so that it is easier to read.

ADD REPLYlink written 3.0 years ago by Istvan Albert ♦♦ 80k

@Istvan: @jaynaythan has changed the text of the OP completely so the exchange above has become orphan.

ADD REPLYlink written 3.0 years ago by genomax65k
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