esian clustering, count
correlation of genetic and geographical distance and so on.
Thank You in advance!
All the best,
Vojtěch
--
Vojtěch Zeisek
Komunita openSUSE GNU/Linuxu
Community of the openSUSE GNU/Linux
http://www.opensuse.org/
http://trapa.cz/
signature.asc
Description: This is a digitally s
lo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org]
> on behalf of Vojtěch Zeisek [vojtech.zei...@opensuse.org] Sent: 07 November
> 2012 15:37
> To: mailinglist R
> Subject: [R-sig-phylo] Microsatellites
>
> Hello,
> could someone, please, point me to some manual, whe
ath, 0, nchar(sourcePath)
- :
no library trees found in 'lib.loc'
Error in parseArlequin(infile, outfiles, sourcePath) :
could not find function "xmlTreeParse"
So it seems the xmlTreeParse is missing. Or am I doing something very wrong?
Does anyone have any experience
ine. It produces
some results despite the above error, but the results are very far from those
I get using dist() function. And the results don't look realistic.
What do I do wrong? :-)
Have a nice day!
Vojtěch
--
Vojtěch Zeisek
Komunita openSUSE GNU/Linuxu
Community of the openSUSE GNU/
access index for repository
http://bioconductor.statistik.tu-dortmund.de/src/contrib
and installation fails. Same error I get with bioconductor.org
Any idea how to set it correctly?
Have a nice day!
Vojtěch
--
Vojtěch Zeisek
Komunita openSUSE GNU/Linuxu
Community of the openSUSE GNU/Linux
http
W2 1PG
> United Kingdom
> Tel. : 0044 (0)20 7594 3658
> t.jomb...@imperial.ac.uk
> http://sites.google.com/site/thibautjombart/
> http://adegenet.r-forge.r-project.org/
> ____
> From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-pro
as calculating PCA/PCoA from any distance. ;-)
For now I don't see any enough good solution, but I at least understand it
more. :-)
> Cheers
> Thibaut
Have a nice day,
Vojtěch
>
> From: r-sig-phylo-boun...@r-project.org [r-sig-phyl
o I do wrong? Is there any better way, how to calculate bootstraps for
microsatellite data?
Sincerely,
Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/
Institute of Botany, Acad
ay, if I don't fix it, PHYLIP is next
choice...
All the best,
Vojtěch
> On Oct 14, 2013, at 9:14 AM, Vojtěch Zeisek wrote:
> > Hello,
> > I know this is FAQ, but I still haven't found solution, which would work
> > for me... :-( I'd like to get unrooted bootstra
Hi, Emmanuel, thank You very much!
Dne Út 15. října 2013 21:45:12, Emmanuel Paradis napsal(a):
> Hi Vojtěch,
>
> Le 14/10/2013 23:14, Vojtěch Zeisek a écrit :
> > Hello,
> > I know this is FAQ, but I still haven't found solution, which would work
> > for me
Yes, that's it, thank You very much, Emmanuel! Sincerely, Vojtěch
Dne St 16. října 2013 14:39:28, Emmanuel Paradis napsal(a):
> Le 16/10/2013 00:20, Vojtěch Zeisek a écrit :
> > Hi, Emmanuel, thank You very much!
> >
> > Dne Út 15. října 2013 21:45:12, Emmanuel Paradis
" 55.8917 37.3167 big yellow Ka 19
[...]
I wasn't able to find how to plot also names of populations along the point and
some legend summarizing symbols used to label populations.
Could someone, please, point me to right way how to do it?
All the best,
Vojtěch
--
Vojtěch Zeisek
h
h=souradnice2$symbol,
> > col=souradnice2$col, cex=2)
>
> text(souradnice2$X.lon, souradnice2$X.lat, labels = souradnice2$char)
>
>
> More info here:
>
> http://stat.ethz.ch/R-manual/R-devel/library/graphics/html/text.html
>
> Hope this helps,
>
> Bier
- Liam
>
> Liam J. Revell, Assistant Professor of Biology
> University of Massachusetts Boston
> web: http://faculty.umb.edu/liam.revell/
> email: liam.rev...@umb.edu
> blog: http://blog.phytools.org
>
> On 1/13/2014 12:14 PM, Vojtěch Zeisek wrote:
> > Hello,
&g
ree, part=pp, rooted=FALSE)
return(ans)
}
It shouldn't be difficult to modify it for little bit different data and/or
use.
Of course, if You find a bug, I'd be very glad to know about it. ;-)
All the best,
Vojtěch
Dne St 16. října 2013 14:39:28, Emmanuel Paradis napsal(a):
>
Zeisek
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/
Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ
http://www.ibot.cas.cz/en/
Czech Republic
t
file formatted in the same way for diploids, it works perfectly...
Any ideas how to fix that?
Thank You in advance,
Vojtěch Zeisek
Dne Pá 30. května 2014 03:34:49 jste napsal(a):
> Hi there,
>
> yes, adegenet handles any (constant) ploidy for most purposes. For input
> formats etc.
="/" and ploidy=3.
>
> Cheers
> Thibaut
> ________
> From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org]
> on behalf of Vojtěch Zeisek [vo...@trapa.cz] Sent: 30 May 2014 10:17
> To: mailinglist R
> Subject:
, I focus on AFLP.
> > As I told you there is much more thing availlable for microsatelites.
> > Benjamin
> >
> > Le Vendredi 30 Mai 2014 09:17 GMT, Vojtěch Zeisek a
écrit:
> >> Hello,
> >> thank You both. poppr looks interesting, I need to explo
ontain missing data. I checked all point and I
don't see any problem... :-( Any idea how to fix it?
BTW, poppr's manual speak about parameter B for number of bootstraps for
bruvo.boot() function, but its manual speaks about parameter sample, which is
the correct one. ;-)
Sincerely,
Vo
.r-project.org/
> >
> > Please feel free to use the adegenet forum for adegenet-related questions.
> > Cheers
> > Thibaut
> >
> >
> >
> > From: r-sig-phylo-boun...@r-project.org
> > [r-sig-phylo-boun...@r-project.org]
s. But right now, I focus on AFLP. As I
> told you there is much more thing availlable for microsatelites. Benjamin
>
> Le Vendredi 30 Mai 2014 09:17 GMT, Vojtěch Zeisek a écrit:
> > Hello,
> > thank You both. poppr looks interesting, I need to explore it more.
> > Adegenet is f
gt; > Yes it is possible in R, there is a package created for related purposes:
> > poppr or something like that… The dev version on github should be
> > preferred. I have seen several R work with polyploids and microsatelites,
> > unfortunately… I work with ALFP :p Benjamin
; is designed for mixed ploidy levels. But right now, I focus on AFLP. As I
> > told you there is much more thing availlable for microsatelites. Benjamin
> >
> > Le Vendredi 30 Mai 2014 09:17 GMT, Vojtěch Zeisek a
écrit:
> > > Hello,
> > > thank You
issing value where
> TRUE/FALSE needed ?
>
> Any ideas?
What was the original command? It looks to me like You forget to use some
required parameter.
> Kind regards,
>
> Stuart
All the best,
Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Scienc
oun...@lists.r-forge.r-project.org
> [adegenet-forum-boun...@lists.r-forge.r-project.org] on behalf of Vojtěch
> Zeisek [vo...@trapa.cz] Sent: 13 July 2014 21:18
> To: Adegenet R-Forum
> Subject: [adegenet-forum] Not working Monmonier
>
> Hello,
> I tried Monmonier analysis as d
ill. Monmonier relies on a
> tesselation, and this tesselation will differ each time you jitter your
> coordinates. Cheers
> Thibaut
>
> From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org]
> on behalf of Vojtěch Zeisek
horeline. Thus, I
> > measured the distances and provide an own matrix of geographic
>
> distances.
>
> > My question is: Can I also install own measured geographic distances
> > instead of coordinates?
>
> Sure, just as Dgeo use matrix o distances along shore
ed at functions in ape
and phangorn, but they seem to work on only one phylogenetic tree or on
distance matrix. I want to get a species tree, but with (possible)
reticulations. Can I do this?
Sincerely,
Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Ch
Hello,
thank You, I overlooked that function. Yes, that is what I'm looking for.
Sincerely,
Vojtěch
Dne Po 3. listopadu 2014 10:23:32 jste napsal(a):
> Hello Vojtěch,
>
> have you looked into consensusNet in phangorn?
>
> Regards,
> Klaus
>
> Am 03.11.2014
pecies
tree out of gene trees?
Sincerely,
Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/
Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ
http://w
o You, please, have
some reference?
> best
>
> Andrés
Thank You,
Vojtěch
> 2014-11-05 13:03 GMT-02:00 Vojtěch Zeisek :
> > Hello,
> > I'm looking for approaches how to get a species tree from set of gene
> > trees. I
> > was looking at Phybase package
lans to restart the development of his package.
>
> Cheers,
> -- François
>
> On Wed, Nov 5, 2014 at 10:48 AM, Vojtěch Zeisek wrote:
> > Dne St 5. listopadu 2014 13:39:49 jste napsal(a):
> > > Hi I installed and used 1.3 recently (under Ubuntu 14.04). I am no
> > &
; an old package version, but the minor "downside" that maintaining the
> functions' code is then up to you.
>
> HTH,
> Dan.
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botan
x27;m looking for something like this in R...
> best
All the best,
Vojtěch
> 2014-11-05 13:48 GMT-02:00 Vojtěch Zeisek :
> > Dne St 5. listopadu 2014 13:39:49 jste napsal(a):
> > > Hi I installed and used 1.3 recently (under Ubuntu 14.04). I am no
> > > expert
&g
e wrong?
Sincerely,
Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/
Institute of Botany, Academy of Science
Zámek 1, Průhonice, 25243, CZ
http://www.ibot.cas.cz/en/
Cze
by coercion
> 3: In nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, ... :
> ...
> When I tried with trees from *.trprobs files, it worked perfectly. Any idea
> what could be wrong?
> Sincerely,
> Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, F
t me know.
Function ppca from package adephylo.
> Thanks in advance.
>
> Best regards,
> Sérgio.
Regards,
Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http://botany.natur.cuni.cz/en/
ttps://stat.ethz.ch/mailman/listinfo/r-sig-phylo
>Searchable archive at
>http://www.mail-archive.com/r-sig-phylo@r-project.org/
--
Vojtěch Zeisek
http://trapa.cz/cs
___
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/
FUEL
>Departamento de Biologia Animal e Vegetal
>Universidade Estadual de Londrina
>Rodovia Celso Garcia Cid, PR 445 Km 380, Campus Universitário
>Caixa postal 10.011
>CEP: 86057-970
>Londrina, Paraná, Brasil
>CV:
>http://buscatextual.cnpq.br/buscatextual/visualizacv
ed package: IRanges
Loading required package: XVector
You do not need Biostrings to use read.newick.
Note there is also read.tree in ape package reading trees in Newick format.
> Thanks a lot for any useful answer!
>
> Gabriela, Charles University in Prague
Sincerely,
Vojtěch
--
Vojtěc
2.3 (2015-12-10) -- "Wooden Christmas-Tree"
> packageVersion("phytools")
[1] ‘0.5.10’
> packageVersion("Biostrings")
[1] ‘2.38.3’
And I do not see any dependency for Biostrings in phytools...
> If I try to load Biostrings I receive an error message that Bio
y=NJ, x=LOCI, FUN=function(X) nj(dist(loci2genind(X))),
B00)
|| 1%Error in df2genind(as.matrix(x[, attr(x, "locicol")]), sep = "[/\\|]",
:
length of factor pop differs from nrow(X)
Any idea what could went wrong?
Thank You,
Vojtěch
--
Vojtěch Zeisek
http://trapa.cz/en/
Departme
BOOT <- boot.phylo(phy=NJ, x=LOCI, FUN=foo, B=1000)
>
> BTW, I don't know if using dist() on a "genind" object is something
> really meaningful. Maybe you want to use another distance function from
> adegenet or another packae (eg, poppr). Anyway, the above trick
tually let me correct myself. The XML dump would be placed in a
> >> publicly accessible archive (because this is one of our public wikis),
> >> likely in a NESCent collection we are putting together on Zenodo (see
> >> https://zenodo.org/collection/user-nescent). The XML dum
t from the original thread, which is from
> about a year ago. Here it is for your reference:
> http://www.mail-archive.com/r-sig-phylo@r-project.org/msg03877.html
>
> -hilmar
>
> > On Jun 7, 2016, at 8:12 AM, Vojtěch Zeisek wrote:
> >
> > Hello,
> > does thi
ins of
>bacteria in my data, the resulted tree is not very clear. The branch
>labels are so much overlapping that they cannot be read at all. Is
>there any way, I can get a neat tree with clearly read labels? Any
>guidance will be very much appreciated.
>
>Regards,
tree? I have tried to change the height and width but
> it’s not working.
--
Vojtěch Zeisek
https://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University in Prague
Benátská 433/2, Prague, 12801, CZ
https://www.natur.cuni.cz/biology/botany/
https://erasmusclub.natur.cuni.cz/
016-10-31) -- "Sincere Pumpkin Patch"
> >>> Copyright (C) 2016 The R Foundation for Statistical Computing
> >>> Platform: x86_64-apple-darwin13.4.0 (64-bit)
> >>> ...
> >>> [R.app GUI 1.68 (7288) x86_64-apple-darwin13.4.0]
> >>>
t install the testing version from ape-package.ird.fr (maybe
> mostly for users of MacOS with no compiling tools), a simple fix to this
> issue is to run:
>
> fix(read.GenBank)
>
> and replace "http:" by "https:", save and close.
>
> Best,
>
parts, so that they are always larger than the current version number on
> CRAN but less than the upcoming one. Thus, the update mechanism of R
> should work properly if you installed a testing version.
>
> Best,
>
> Emmanuel
>
> Le 21/11/2016 à 17:59, Vojtěch Zeisek a écrit
re 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.natur.cuni.cz/biology/botany/
Institute of Botany, Czech Academy of Sciences
Průhonice, Czech Republic
the hint. This is simple, but it doesn't align the tip labels. I
need some optimization to align same labels as close together as possible. I
see it like last instance if other options fail.
I'll explore rest of the options now. :-)
> On Tue, Apr 25, 2017 at 12:20 PM, Vojtěch
blog:
> http://blog.phytools.org/2017/04/showing-multiple-conflicting.html. Let
> me know if any of them work for you.
>
> All the best, Liam
>
> On 4/25/2017 12:20 PM, Vojtěch Zeisek wrote:
> > Hello,
> > for comparison of two trees I can use very nice function cophyl
gt; > xlim
> > & ylim, then plotTree will reset these values for each new plotted tree.
> >
> > Later this evening I will do my best to make an example & post it to my
> > blog.
> >
> > - Liam
> >
> > On 4/25/2017 12:20 PM, Vojtěch Zeisek
was
> specific to the 10 taxon case. Let me know if that helps.
>
> On 4/26/2017 11:48 AM, Vojtěch Zeisek wrote:
> > Hello,
> > Liam, thank You very much! It is what I was looking for. Unfortunately, I
> > have problem with Your solution 4 and onward (attached). Previous 3
> >
Hi there,
>
> treespace would be an alternative, but its usefulness for 5 trees will
> be quite limited. Just in case:
> https://github.com/thibautjombart/treescape
>
> Cheers
> Thibaut
>
> On 25 April 2017 at 18:20, Vojtěch Zeisek wrote:
> > Hello,
> > for c
be installed from GitHub
> using devtools.
>
> - Liam
>
> On 4/26/2017 12:18 PM, Vojtěch Zeisek wrote:
> > Yes, it helps and makes the tree in good scale. Just branches of one tree
> > do not reach the right edge like the others. And tip labels are still
> > miss
in are stored in
binary format, I'm bit struggled here... :(
Any idea how to remove columns with given portion of "N" in sequences?
Sincerely,
V.
--
Vojtěch Zeisek
https://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University, Prague, Czech Republic
https://www.
sequences in DNAbin are stored
> in binary format, I'm bit struggled here... :(
> Any idea how to remove columns with given portion of "N" in sequences?
> Sincerely,
> V.
--
Vojtěch Zeisek
https://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University, Pr
.matrix(seq)
> temp <- seq %>% sapply(.,grep,pattern="n") %>% unlist(.,use.names=F) %>%
> table
> seq[,-(names(temp)[which(temp/ncol(seq)>thresh)] %>% as.integer)]
>
> Greetings,
> Andreas
>
> Am 2017-10-27 16:25, schrieb Vojtěch Zeisek:
> &
hack the function. For instance, if
> you want to find the sites with R/Y, first, get the integer codes:
>
> R> as.integer(as.DNAbin("R"))
> [1] 192
> R> as.integer(as.DNAbin("Y"))
> [1] 48
>
> Then, change the above line for:
>
> foo &
approach you use, all coloumns are filtered out if
> you filter all coloumns containing N.
> Please open your alignment in a text editor or use
> image.DNAbin(youralignment) to visualise your alignment before you
> process it in any way.
> Best wishes,
> Andreas
>
> Am
with
the 'power' parameter. I was able to get good output, but I wonder if there is
some possibility to do this automatically. Might be something like
use.edge.length=FALSE in ape::cophyloplot (about phytools::cophylo I like the
automatic rotation and curved connecting lines).
Sincere
#x27;power.'
> 0 time & may look better than the default.
> All the best, Liam
>
> On 12/12/2018 12:07 PM, Juan Antonio Balbuena wrote:
> > You can try this:
> > tree<- compute.brtime(tree, tree$Nnode:1)
> > It will produce an ultrametric tree with it
prefer?
> All the best, Liam
>
> On 12/12/2018 6:29 PM, Vojtěch Zeisek wrote:
> > Hello,
> > the original question was
> > https://www.mail-archive.com/r-sig-phylo@r-project.org/msg05367.html
> > Playing with the 'power' parameter of the compute.brlen()
sonly(), but it didn't
lead to success. I haven't found any other way how to trim protein alignment
in R similar to what these two function do. Is there any way?
Sincerely,
V.
--
Vojtěch Zeisek
https://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University, Prague, Czech
gt; Franz
>
> > On 2. Nov 2021, at 11:38, Vojtěch Zeisek wrote:
> > Hello,
> > I try to trim protein alignments in R. I see del.colgapsonly() and
> > del.rowgapsonly() from ape can trim only class DNAbin. As DNAbin as
> > basically same matrix as AAbin (Isn&
foo <- function(x) sum(x == 4)
> by:
> foo <- function(x) sum(x == 0x58)
> That sh(c)ould do it.
> Best,
> Emmanuel
>
> Le 2 Nov 21, à 17:37, Vojtěch Zeisek vo...@trapa.cz a écrit :
> > Hello,
> > I try to trim protein alignments in R. I see del.col
ape::trans). So this line 7 should be:
> foo <- function(x) sum(x == 0x58 | x == 0x2d)
> Or (probably easier to modify):
> foo <- function(x) sum(x == charToRaw("X") | x == charToRaw("-"))
> Cheers,
> Emmanuel
>
> Le 2 Nov 21, à 19:23, Vojtěch
;) : cannot open the connection
So obviously there is change in command line parameters among MUSCLE versions
3.8 and 5.1. I hope it would be an easy fix. :-)
Sincerely,
V.
--
Vojtěch Zeisek
https://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University, Prag
my testing it works
well. I'm not sure if tryCatch is really needed there. In any case,
improvements welcomed. :-)
So, what do You think? Is this usable improvement of ape::dist.topo?
Sincerely,
V.
--
Vojtěch Zeisek
https://trapa.cz/en/
Department of Botany, Faculty of Science
Charles Univ
int, thank You.
> So with great power comes great responsibility
> and users should read the man pages.
> Kind regards,
> Klaus
>
> On Mon, Mar 6, 2023 at 2:43 PM Vojtěch Zeisek wrote:
> > Hello dear colleagues,
> > I use often ape::dist.topo (see here dist.topo.r), wh
s plain lapply) for cores==1, while parallel and doParallel
> > for multiple cores. It also contains some checks and error handling.
> > From my testing it works well. I'm not sure if tryCatch is really
> > needed there. In any case, improvements welcomed. :-)
> > So, wha
gt; https://github.com/emmanuelparadis/ape
> I had a quick look at your code and these are interesting improvements.
> It seems also possible to improve the basic code of dist.topo() (e.g.,
> using bitsplits) so it is worth opening an issue.
> Cheers,
> Emmanuel
>
> - Le 6 Mar
ived project? And when I started working on this little bit (rather
maintenance fixes than "big" development), are there any general comments or
requests about kdetrees?
Sincerely,
V.
--
Vojtěch Zeisek
https://trapa.cz/en/
Department of Botany, Faculty of Science
Charles University
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