? 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, Prague, Czech Repu
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 M
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, what do You think? Is this usable improveme
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), which is doing
. 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 University, Prague, Czech Republic
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, Prague, Czech Republic
h
s). 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 Zeisek vo
m(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.colgapsonly() and
> &g
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'
(), 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 Republic
https
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).
Sincerely,
V.
--
oach 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 2017
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 <- funct
ix(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:
&
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, Prague,
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.natur
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
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 <vo...@trapa.cz> wrote:
> >
,11) (that 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
> >
For instance, unless we set
> > 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
> >
> >
p://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 cophyloplot
> >
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 Zeisek <vo..
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.natur.cuni.cz/biology/botany/
Institute of Botany, Czech Academy of Sciences
Průhonice, Czech Republic
http
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 :
>
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,
>
&g
R. But, since I have got 220 strains 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.
&g
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 <vo...@trapa.cz> wrote:
> >
> > Hell
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 will be
> useful in all cases s
kage: 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
--
Vojtěch Zeisek
http://trapa.cz/en/
Department
:-) And You'd need to modify
instlib according to Your placement.
> I am running R v 3.2.3 and phytools v 0.5-10.
$ R --version
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
> packageVersion("phytools")
[1] ‘0.5.10’
> packageVersion("Biostrings")
[1] ‘2.3
=K4211230P7
[[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-phylo@r-project.org/
--
Vojtěch Zeisek
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.do?id=K4211230P7
2015-08-26 11:31 GMT-03:00 Vojtěch Zeisek
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/
Institute of Botany, Academy of Science
, ... :
NAs introduced 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, Faculty
--
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
signature.asc
?
best
Andrés
Thank You,
Vojtěch
2014-11-05 13:03 GMT-02:00 Vojtěch Zeisek vo...@trapa.cz:
Hello,
I'm looking for approaches how to get a species tree from set of gene
trees. I
was looking at Phybase package https://code.google.com/p/phybase/ but it
seems
to be abandoned and when I
,
-- François
On Wed, Nov 5, 2014 at 10:48 AM, Vojtěch Zeisek vo...@trapa.cz 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
expert
and I can help you further but I wanted to assure you the package is
working fine
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
Charles
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 03:10 schrieb Vojtěch Zeisek vo...@trapa.cz
-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 described in Adegent tutorial. I'm not
familiar with that method (for similar question I used IMa2 last
?
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 Science
Charles University in Prague
Benátská 2, Prague, 12801, CZ
http
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,
Vojtěch Zeisek
Dne Čt 29. května 2014 16:12:31 jste napsal
... :-( 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,
Vojtěch Zeisek
Dne Čt 29. května 2014 16:12:31 jste napsal(a):
Hi,
Yes
: r-sig-phylo-boun...@r-project.org
[r-sig-phylo-boun...@r-project.org] on behalf of Gilles Benjamin Leduc
[g...@hi.is] Sent: 29 May 2014 17:12
To: Vojtěch Zeisek
Cc: mailinglist R
Subject: Re: [R-sig-phylo] Triploid microsatellites?
Hi,
Yes it is possible in 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: Re: [R-sig-phylo] Triploid microsatellites?
Hello,
thank You both. poppr looks interesting, I need to explore it more.
Adegenet is famous package. I
, 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):
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 napsal(a):
Hi
://blog.phytools.org
On 1/13/2014 12:14 PM, Vojtěch Zeisek wrote:
Hello,
I have probably very silly question about maps of samples, but I'm not
able to figure it out. :-( I wish to generate simple map showing sampling
localities of sampled populations, with various symbols and colors
(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
On Jan 13, 2014, at 10:14 AM, Vojtěch Zeisek vo...@trapa.cz wrote:
Hello,
I have probably very silly question
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 napsal(a):
Hi Vojtěch,
Le
-project.org/
From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org]
on behalf of Vojtěch Zeisek [vojtech.zei...@opensuse.org]
Sent: 07 June
2013 15:46
To: mailinglist R
Subject: [R-sig-phylo] PCoA with custom distance matrix
Hello
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-phylo-boun...@r-project.org]
on behalf of Vojtěch Zeisek [vojtech.zei...@opensuse.org]
Sent: 10
, 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/Linux
http://www.opensuse.org/
http://trapa.cz/
signature.asc
Description
to 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
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 signed
[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, where I can learn how to
work with microsatellite data
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