Re: [R-sig-phylo] chronos ape substitution rate strict clock

Dear Vincenzo, For ML estimates the edge length are the expected number of substitutions per site, which depends on the product of rate and time. So you need either a rate estimate or calibration points to estimate the time. If you divide the edge length by the rate the edges should be

Re: [R-sig-phylo] Parallelization in ape::dist.topo

-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus Schliep Senior Scientist Institute of Molecular Biotechnology TU Graz https://www.imbt.tugraz.at [[alternative H

Re: [R-sig-phylo] ancestral state reconstruction with a complex discrete, trait

> > R-sig-phylo mailing list > > R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > [[alternative HTML version deleted]] > > _______ > R-sig-phylo mail

Re: [R-sig-phylo] dist.nodes

-phylo mailing list - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > ___ > R-sig-phylo mailing list - R-sig-phylo@r

Re: [R-sig-phylo] Using bind.tip and lapply on a multiPhylo object

ases computation time and if I am reinventing the wheel > it would be nice to know if I am overthinking things. > > Sincerely, > Russell > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-pro

Re: [R-sig-phylo] phangorn

tp://www.mail-archive.com/r-sig-phylo@r-project.org/ > -- Klaus Schliep Senior Scientist Institute of Computational Biotechnology TU Graz https://icbt.tugraz.at https://www.phangorn.org/ <http://www.phangorn.org/> [[alternative HTML version deleted]]

Re: [R-sig-phylo] extracting sister taxon pairs from phylo object in APE R package

-project.org > > > https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-sig-phylodata=02%7C01%7Cliam.revell%40umb.edu%7C90a597b4b91d49de99c908d79571b556%7Cb97188711ee94425953c1ace1373eb38%7C0%7C1%7C637142187929623185sdata=xiGcF2HLz%2Ffv6

Re: [R-sig-phylo] Testing tree disagreement: SH-test disappeared in ape-package

Hi Sebastian, there is an implementation of the SH-test and SOWH-test in phangorn. Send me an mail off list if you have problems using them. Regards, Klaus On Jun 8, 2018 8:50 AM, "Sebastian Y. Müller" wrote: Dear all, I'd was wondering how to best perform a test to determine test disagreement

Re: [R-sig-phylo] importing trees from birdtree.org into R

stituto de > Biociências, USP. > Rua do Matão, trav. 14, nº 321, Cidade Universitária, > São Paulo - SP, CEP: 05508-090, Brasil. > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mai

Re: [R-sig-phylo] Rescaling a cophenetic matrix based on the Early Burst Model?

t.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > > > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.

Re: [R-sig-phylo] Possible Bug in ape::read.tree

-02-06 CRAN (R 3.4.1) >>> parallel 3.4.1 2017-06-30 local >>> prettyunits 1.0.2 2015-07-13 CRAN (R 3.4.1) >>> progress 1.1.2 2016-12-14 CRAN (R 3.4.1) >>> R62.2.2 2017-06-17 CRAN (R 3.4.0) >>> Rcpp 0.12.12 2017-07-15 CRAN (R 3.4.0) >>>

Re: [R-sig-phylo] selecting a set of incongruent trees from a posterior distribution

; > > sig-ph...@r-project.org/ > > > > > > > [[alternative HTML version deleted]] > > > > > > > > -- > > > > Subject: Digest Footer > > > > ___ >

Re: [R-sig-phylo] A possible alternate MRCA function to APE's getMRCA

NULL) >>>Ntip <- length(phy$tip.label) >>>rootnd <- Ntip + 1L >>> >>>pars <- integer(phy$Nnode) # worst case assignment, usually far too >>> long >>>mrcaind <- 1L # index in pars of the mrca node. will return highest >

Re: [R-sig-phylo] A possible alternate MRCA function to APE\'s getMRCA

t;> Libre de virus. www.avast.com > >>> <https://www.avast.com/sig-email?utm_medium=email_ > source=link_campaign=sig-email_content=emailclient> > >>> > >>> > >>> > >>> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > >>> > &

Re: [R-sig-phylo] A possible alternate MRCA function to APE's getMRCA

} > idx <- which(pars == cpar); > if (idx > mrcaind) { > mrcaind <- idx; > } > done <- TRUE; > } else { > # keep going! > c

Re: [R-sig-phylo] Graphically comparing multiple trees

hope there is some more automated way to do it. > > >> :-) > > >> Sincerely, > > >> V. > -- > Vojtěch Zeisek > https://trapa.cz/en/ > > Department of Botany, Faculty of Science > Charles University, Prague, Czech Republic > https://www.nat

Re: [R-sig-phylo] Graphically comparing multiple trees

> Searchable archive at http://www.mail-archive.com/r- >> sig-ph...@r-project.org/ >> >> > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at h

Re: [R-sig-phylo] distances between the nodes

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta >> >> VAT-ID No.: DE143293537 >> >> >> >> ___ >> R-sig-phylo mailing list - R-sig-phylo@r-project.org >> https://stat.ethz.ch/mailman/listi

Re: [R-sig-phylo] Enigmatic error with drop.tip

+ > > _______ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoct

Re: [R-sig-phylo] multi2di fails on multiPhylo objects

R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.p

Re: [R-sig-phylo] phylo from igraph

ancouver, Canada > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig

Re: [R-sig-phylo] Midpoint root a tree with root() function ape ver 4.0

> ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ -- Klaus Schliep Postdoctoral Fello

Re: [R-sig-phylo] compressTipLabel as an option to read.trees()

-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phang

Re: [R-sig-phylo] concatenating loci with different taxa

ig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r- > sig-ph...@r-project.org/ > -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston http://www.phangorn.org/ [[alternati

Re: [R-sig-phylo] Anyone knows how to concatenate aligned genes sequences so as to create whole genome alignments?

Dear Rav, write.dna() from ape just does this. Klaus On Sep 12, 2016 9:07 AM, "Bhuller, Ravneet" < ravneet.bhulle...@imperial.ac.uk> wrote: > Hi Thibaut, > > Is there anyway I can save the concatenated alignment (created using apex > and the concatenate function) in FASTA format? > > Regards, >

Re: [R-sig-phylo] Ultrametric tree not recognized

> > The default is: is.ultrametric(phy, tol = .Machine$double.eps^0.5). > According to ?.Machine this value does not depend on the machine precision. > On my laptop, it gives: > > R> .Machine$double.eps^0.5 > [1] 1.490116e-08 > > Best, > > Emmanuel > > > L

Re: [R-sig-phylo] Ultrametric tree not recognized

f Ecology & Evolutionary Biology > Room 2071, Kraus Natural Sciences Building > Ann Arbor MI 48109-1079 > josep...@umich.edu > > > > On 16 Aug, 2016, at 10:15, Klaus Schliep <klaus.schl...@gmail.com> wrote: > > Hello all, > this may come be surprising to many,

Re: [R-sig-phylo] Ultrametric tree not recognized

Hello all, this may come be surprising to many, but consulting the manual ?is.ultrametric can be helpful. Why not simply try e.g. is.ultrametric(tree, tol=.01) So in this sense RTFM Regards, Klaus On Aug 16, 2016 9:31 AM, "Martin Dohrmann" wrote: > > Am

[R-sig-phylo] Nantucket phylogeny developeR bootcamp

of the workshop, course leaders Drs. April Wright and Klaus Schliep (with Dr. Liam Revell participating remotely) will provide an introduction to the primary data structures and methods of common phylogenetic R packages, the basics of computational algorithms for phylogenies, and an overview of package

Re: [R-sig-phylo] Error in plotBS when number of taxa is small

HI Kamilla, can you send me your code and data and what phangorn version are you using? Cheers, Klaus On Tue, Jun 14, 2016 at 6:42 PM, Kamila Naxerova wrote: > Hi all, > > I am trying to attach bootstrap values to a small tree (just 4 taxa). > plotBS() in the phangorn

Re: [R-sig-phylo] new testing version of ape

> Emmanuel > > > > ___ > > R-sig-phylo mailing list - R-sig-phylo@r-project.org > > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > Searchable archive at > > http://www.mail-archive.com/r-sig-phylo@r-project.org/ > > >

Re: [R-sig-phylo] colouring tree branches like tips

gt; Thanks a lot for any help. > > > Best regards > > > G > > > > Gudrun Gygli, MSc > > PhD candidate > > Wageningen University > Laboratory of Biochemistry > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > Phone 31 317483387 > e-mail: gudrun.gy...@wur.nl &

Re: [R-sig-phylo] colouring tree branches like tips

li, MSc > > PhD candidate > > Wageningen University > Laboratory of Biochemistry > Dreijenlaan 3 > 6703 HA Wageningen > The Netherlands > > Phone 31 317483387 > e-mail: gudrun.gy...@wur.nl > > - - - - - - - - - - - - - - - - - - > > Project information:

Re: [R-sig-phylo] extract parent-child from newick

gt; Johnson City TN 37614-1710 > Cell 423-676-7489 > Office/lab 423-439-4359 > Fax423-439-5958 > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > S

Re: [R-sig-phylo] Package phytools load failed

Hi all, you have to install the Biostrings package from bioconductor. Than it should works. Phangorn has a dependency on biostrings and phytools depend on phangorn. Have a nice weekend Klaus Am 09.01.2016 16:35 schrieb "Donald Miles" : > Dear All, > > I receive the same error

Re: [R-sig-phylo] Calculating branch lengths on a multiphylo object

uot; > > fit.equal<-t(mapply(fit.model,trees,xy)) > Error in mapply(fit.model, trees, xy) : object 'xy' not found > > mean(fit.equal[,1]) ## should be zero > Error in mean(fit.equal[, 1]) : object 'fit.equal' not found > > Does anyone have any advice? Please let me

Re: [R-sig-phylo] Detecting homoplasy

Dear Tim, I added an optional argument sitewise to the CI and RI function in phangorn. The vector may contains NaN if the function is undefined: pscore of 0 for CI, uninformative site for RI. It is now on github: library(devtools) install_github("KlausVigo/phangorn") Cheers, Klaus On Thu, Dec

[R-sig-phylo] Problems with dependency Biostrings

any bioconductor packages, chances are that you also installed Biostrings package are pretty high. Regards, Klaus -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[alternative HTML version deleted]] ___ R-sig-p

Re: [R-sig-phylo] Mapping gene gain loss info to rooted species tree

530) 574-5134 | LinkedIn <http://www.linkedin.com/in/anandksrao> > _ > CTTATTGTTGAACTTOAATGGTGCTAATGATCCTCGTOTCTCCTGAACGT - translate THAT! > > [[alternative HTML version deleted]] > > ___

Re: [R-sig-phylo] output of phangorn::midpoint is not compatible with ape::ladderize?

--~~~--~~--~--~--- > > [[alternative HTML version deleted]] > > ___ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at &g

Re: [R-sig-phylo] Cannot plot above 500 superimposed trees with densiTree (Phangorn)

deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab

Re: [R-sig-phylo] Plotting error edgelabels in phylogeny type=fan

-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig

Re: [R-sig-phylo] Prune very large tree

HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow

Re: [R-sig-phylo] Bug in reorder.phylo() (related to cleaning phylo objects)

___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston

Re: [R-sig-phylo] Phylogenetic analysis with sequencing error

]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston

Re: [R-sig-phylo] Problem loading phytools on Mac

list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[alternative HTML version deleted

Re: [R-sig-phylo] phangorn - midpoint function

-sig-phylo Searchable archive at http://www.mail-archive.com/r- sig-ph...@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[alternative HTML version deleted]] ___ R-sig-phylo mailing list

Re: [R-sig-phylo] Identify nodes along a pathway from root to a given tip

Hello Manabu, try Ancestors from phangorn. Regards Klaus Am 04.11.2014 08:12 schrieb Manabu Sakamoto manabu.sakam...@gmail.com: Dear list, I was wondering if there was an existing function to identify all the nodes (e.g., phylo$edge[,1]) along a pathway from the root to any given tip. I've

Re: [R-sig-phylo] Network from gene trees

Hello Vojt�ch, have you looked into consensusNet in phangorn? Regards, Klaus Am 03.11.2014 03:10 schrieb Vojt�ch Zeisek vo...@trapa.cz: Hello, let's say I have many gene trees (all have same labels) in one multiPhylo object. The trees are not fully congruent. One of the reasons can be

Re: [R-sig-phylo] sitewise parsimony scores with parsimony()

-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University of Massachusetts Boston [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman

Re: [R-sig-phylo] midpoint rooting? how to get the outgroup?

/listinfo/r-sig-phylo // https://stat.ethz.ch/mailman/listinfo/r-sig-phylo // / -- Klaus Schliep Universit� Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris [[alternative HTML version deleted]] ___ R-sig-phylo

Re: [R-sig-phylo] Plotting Posterior Probabilities from MrBayes Trees (An Update)

___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Postdoctoral Fellow Revell Lab, University

Re: [R-sig-phylo] Ape package.

-sig-phylo@r-project.org/ -- Klaus Schliep [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig

Re: [R-sig-phylo] chronos and gammaStat

://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https

Re: [R-sig-phylo] chronos and gammaStat

convert it? Thanks! -- *De:* Klaus Schliep klaus.schl...@gmail.com *Para:* Fabricia Nascimento nasciment...@yahoo.com.br *Cc:* r-sig-phylo@r-project.org r-sig-phylo@r-project.org *Enviadas:* Terça-feira, 8 de Abril de 2014 13:20 *Assunto:* Re: [R-sig-phylo

Re: [R-sig-phylo] Fatal Crash in ancestral.pars in phangorn

and Technology 501 E. St. Joseph Rapid City, SD 57701 http://webpages.sdsmt.edu/~dbapst/ http://cran.r-project.org/web/packages/paleotree/index.html -- Klaus Schliep [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r

Re: [R-sig-phylo] Generate all possible trees for n species

deleted]] ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University

Re: [R-sig-phylo] Midpoint rooting routine?

___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r- sig-ph...@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain http

Re: [R-sig-phylo] Run time for pglmm.fit in picante

___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo

Re: [R-sig-phylo] compar.gee crashing R

___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain http

Re: [R-sig-phylo] Collapsing branches with low bootstrap values

___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain http://darwin.uvigo.es/kschliep

[R-sig-phylo] Fwd: Collapsing branches with low bootstrap values

-- Forwarded message -- From: Klaus Schliep klaus.schl...@gmail.com Date: Thu, Aug 22, 2013 at 6:12 PM Subject: Re: [R-sig-phylo] Collapsing branches with low bootstrap values To: Naxerova, Kamila naxer...@fas.harvard.edu Hi Kamila, try function pruneTree in phangorn. data

Re: [R-sig-phylo] getting a list of clusters with their associated bootstrap support

Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain http://darwin.uvigo.es/kschliep/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list

Re: [R-sig-phylo] Incongruence

archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain http://darwin.uvigo.es/kschliep/ [[alternative HTML version deleted]] ___ R-sig-phylo mailing list - R-sig

Re: [R-sig-phylo] Very simple question on fitted values and scatterplots

[ at ] mpi-cbg.de **---* [[alternative HTML version deleted]] -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https

Re: [R-sig-phylo] read.nexus.data parser

-project.org/ ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University

Re: [R-sig-phylo] problem with drop.tip

://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http

Re: [R-sig-phylo] problem with drop.tip

in 1:1000){print(i);write.tree(tr2[[i]])} # may helps find you the trees which fail write.tree(tr2, file=result.tre) Cheers, Klaus On 2/28/13, Klaus Schliep klaus.schl...@gmail.com wrote: Dear John, can you please be a bit more specific with your error message. It is always good to have

Re: [R-sig-phylo] Does anyone know about a function to remove redundancy from a database?

/profile/Luiz_Fagundes_de_Carvalho/?ev=prf_info [[alternative HTML version deleted]] -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman

Re: [R-sig-phylo] issue with cophenetic.phylo()

://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org

Re: [R-sig-phylo] estimating mutation rates

://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Phylogenomics Lab at the University of Vigo, Spain ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] problem with boot.phylo() and sample order randomisation

Hi Alastair, I discovered two problems with the analysis. One is your data, which contains too many transitions and so you lost most of the information about your the process which generated the data. There is also a problem with prop.clades, which does not take care enough for different

Re: [R-sig-phylo] R package for detecting positive selection?

/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6

Re: [R-sig-phylo] Cophenetic repeats

Hello Ben, is your tree ultrametric? Do you have a e.g. UPGMA tree? This would explain your observation. You can test your tree with is.ultrametric(trx). Regards, Klaus On 5/27/12, Ben Weinstein bwein...@life.bio.sunysb.edu wrote: Hi all, I'm trying to decide if this an R error, or an

Re: [R-sig-phylo] center of tree

-- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] treefinder chronogram problems

Hello John, it seems the chronogram contains the heights instead of the edge.lengths for each edge. Here is a small function to convert the tree. You should check if it is the same as in treefinder. convert.tree - function(tree){ el = numeric(max(tree$edge)) el[tree$edge[,2]] =

Re: [R-sig-phylo] parsimony bootstrapping

Hello Brian, it is quite easy: trees = bootstrap.phyDat(primates, pratchet, trace = 0) plotBSNew(treeRatchet, trees) You can use the same parameters as for pratchet and there is some support for parallel code if you run it on a terminal (on Linux or Mac). Unfortunately there is was a bug

Re: [R-sig-phylo] Zero bootstrap values

Dear Gwennaël, the bootstrapping function is fine, it is just a problem with the plotting. Can you try this function, it should work: plotBSNew - function (tree, BStrees, type = unrooted, bs.col = black, bs.adj = NULL, ...) { prop.clades - function (phy, ..., part = NULL, rooted = FALSE) {

Re: [R-sig-phylo] Boostrap and likelihood values on branches

Dear Gwennaël, first it seems there was a bug in the function prop.clades from ape introduced recently, results in many zeros of bootstrap values. This function needs to be replaced in the ape package: prop.clades - function (phy, ..., part = NULL, rooted = FALSE) { if (is.null(part)) {

Re: [R-sig-phylo] Estimating branch lengths on a fixed topology from molecular data

Hello Alejandro, you can use the phangorn package to do this in R. The code could look like this: library(phangorn) tree - read.tree(treefile) # load the tree / topology dat - read.phyDat(datafile) # load the data #Parsimony, apply length using the ACCTRAN criterion treeMP - acctran(tree, data)

Re: [R-sig-phylo] phyDat format problem

___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R

Re: [R-sig-phylo] Error message using clustal{ape} under Windows

Dear Gwennaël, it seems it is a problem with the path to clustal, as the path contains spaces. Try clustal(x, exec = shortPathName(C:/Program Files (x86)/ClustalW2/clustalw2.exe)) it works for me. Regards, Klaus On 1/3/12, Gwennaël Bataille gwennael.batai...@uclouvain.be wrote: Dear all, I

Re: [R-sig-phylo] basal dichotomy in phylo object

'phylo'. I tried 'root' function of 'ape' but with no success. I will be grateful for any advice. Best wishes Ondrej Mikula ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep

Re: [R-sig-phylo] Negative Eigenvalues from Phylo Distance Matrix

-- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] phylogenetic tree diameter

-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] phylo to dendrogram

of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et

Re: [R-sig-phylo] outputting values during taxon pruning

https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] Dating trees using date.phylo - ape problem?

not date.phylo... Very best Roland [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie

Re: [R-sig-phylo] Dating trees using date.phylo - ape problem?

at 1:24 PM, Klaus Schliep klaus.schl...@gmail.comwrote: Dear Roland, it would be good if you add the datasets, that one can reproduce your results (archotreeresolved, ages). I would guess from the error message that your ages list may has the wrong format. Also traceback() sometimes tells you

Re: [R-sig-phylo] Dating trees using date.phylo - ape problem?

at 4:10 PM, Klaus Schliep klaus.schl...@gmail.comwrote: Hi Roland, as I suspected, your ages list was not in the right format (has nothing to do with ape). Try this: tmp = read.csv(agescut.csv, header=FALSE) ages = matrix(tmp[, 2], ncol=1) rownames(ages) = tmp[,1] tree = read.tree

Re: [R-sig-phylo] Bootstrap values and NJ when there is no genetic distance between samples

Cell: 082 491-7275 - [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus

Re: [R-sig-phylo] Branch and Bound Maximum Parsimony (Matthew Vavrek)

your analysis. Kind Regards and good luck, Ross Mounce ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard

Re: [R-sig-phylo] sort trees by constraint?

! Just joined the list... looking forward to it! -Brad PhD Student Harvard Herbaria ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Regards, Klaus -- Klaus Schliep Université Paris 6

Re: [R-sig-phylo] bootstrapping with boot.phylo()

very much for your help Gontran Sonet ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris

Re: [R-sig-phylo] bind.tree() error

/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] The Speed of Different Methods For Obtaining the Descendant Tip Taxa per Node

. system.time(desc-Descendants(res_tree,edge_end)) user system elapsed 1.560.001.56 -Dave On Sun, Mar 6, 2011 at 3:22 PM, Klaus Schliep klaus.schl...@gmail.com wrote: Hi David, you can supply Descendents (from phangorn) with a vector instead of using sapply. I

Re: [R-sig-phylo] Error after ladderizing a tree

the phangorn library were exactly what I was looking for. ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005

Re: [R-sig-phylo] Problems with transferring trees back into ape from Mesquite

-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig

Re: [R-sig-phylo] Retention Index

: (+34) 961270967 miguel.ve...@uv.es http://www.uv.es/verducam ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint

Re: [R-sig-phylo] optimizing branch length of a tree topology based on a distance matrix

-- Klaus Schliep Université Paris 6 (Pierre et Marie Curie) 9, Quai Saint-Bernard, 75005 Paris ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

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