[R-sig-phylo] Deadline extension for full talk abstracts for Conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio)
The deadline for submitting abstracts for full talks to the inaugural conference on Informatics for Phylogenetics, Evolution, and Biodiversity (iEvoBio) has been extended by one week to Friday, March 25, 2011. We hope that this will give those interested in contributing sufficient time to do so. Please see http://bit.ly/iEvoBio2011_CfA for the full Call for Abstracts and author instructions. We still expect to be able to notify accepted talks in time for the early registration deadline of iEvoBio (and Evolution). More details about the program and guidelines for contributing content are available at http://ievobio.org. You can also find continuous updates on the conference's Twitter feed at http://twitter.com/ iEvoBio, and there is a Google group you can join at http://groups.google.com/group/ievobio-announce to receive announcements. iEvoBio is sponsored by the US National Evolutionary Synthesis Center (NESCent) in partnership with the Society for the Study of Ecolution (SSE) and the Society of Systematic Biologists (SSB). Additional support has been provided by the Encyclopedia of Life (EOL). The iEvoBio 2011 Organizing Committee: Rob Guralnick (University of Colorado at Boulder) (Co-chair) Cynthia Parr (Encyclopedia of Life) (Co-chair) Dawn Field (UK National Environmental Research Center) Mark Holder (University of Kansas) Hilmar Lapp (NESCent) Rod Page (University of Glasgow) ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] bootstrapping with boot.phylo()
Dear Gontran,
for short sequences such a result can happen. Maybe you check whether
any values in
dist.dna(seq100b, model = raw)
are close to 0.75.
I suspect that some elements in this distance matrix are close to 0.75
than pairwise distances for the bootstrap samples are likely to be
equal or greater than 0.75. Most models (K80, JC69 etc.) are not
defined for distances =0.75 and will return Inf or NaN (the 0.75 can
vary a bit, depending on the substitution model). bionj of course does
not like building trees from infinite values as input. With short
sequences the variances are of course larger and you are more likely
to observe this, that's why your larger data set works fine.
However in this cases NaN or Inf are the correct results!
It would be nice to catch this error with a try and use only trees
from finite distance matrices or set infinite values to a large value.
But one should return a warning as these samples are likely to be
biased.
Kind regards,
Klaus
On 3/15/11, Gontran Sonet gontran.so...@naturalsciences.be wrote:
Dear all,
When I make a bootstrapping analysis of relatively short DNA sequences
(100bp), I have an error message:
Error in bionj(dist.dna(seq100b, model = K80, pairwise.deletion =
FALSE, :
NA/NaN/Inf in foreign function call (arg 1)
I am not able to solve the problem since:
1)This short sequence data set is part of a larger data set where
bootstrapping works perfectly using the same commands:
mytre-bionj(dist.dna(seq100b,model=K80,pairwise.deletion=FALSE,as.matrix=TRUE))
boot.phylo(mytre,seq100b,FUN=function(seq100b) {
bionj(dist.dna(seq100b,model=K80,pairwise.deletion=FALSE,
as.matrix=TRUE))})
2)The problematic data set doesn't contain any - or ? or N, or
ambiguities and the dist.dna() doesn't produce any NA or missing value.
seq100b
396 DNA sequences in binary format stored in a matrix (.
All sequences of same length: 100
Labels: XX, XX, XX
Base composition:
a c g t
0.224 0.281 0.222 0.273
3)This data set also works in other programs (like Mega) without any
problem.
Thank you very much for your help
Gontran Sonet
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--
Klaus Schliep
Université Paris 6 (Pierre et Marie Curie)
9, Quai Saint-Bernard, 75005 Paris
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Re: [R-sig-phylo] bootstrapping with boot.phylo()
Klaus Schliep wrote -- I suspect that some elements in this distance matrix are close to 0.75 than pairwise distances for the bootstrap samples are likely to be equal or greater than 0.75. Most models (K80, JC69 etc.) are not defined for distances =0.75 and will return Inf or NaN (the 0.75 can vary a bit, depending on the substitution model). bionj of course does not like building trees from infinite values as input. With short sequences the variances are of course larger and you are more likely to observe this, that's why your larger data set works fine. However in this cases NaN or Inf are the correct results! I often have to deal with users of my PHYLIP package who are upset at this happening with large distances when the sequences are bootstrapped. (In my package the distance is set to -1.0 in that case, and it should not be used to make a tree). NaN is not the correct value, but Inf is -- the correct distance for (say) the Jukes-Cantor model or the Kimura 2-parameter model when the sequences differ by more than 75% is (positive) infinity, since these are inferred to be unrelated sequences. It would be nice to catch this error with a try and use only trees from finite distance matrices or set infinite values to a large value. But one should return a warning as these samples are likely to be biased. Exactly. J.F. Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
