[R-sig-phylo] Microsatellites

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

Re: [R-sig-phylo] Microsatellites

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

[R-sig-phylo] R & Arlequin (little OT?)

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

[R-sig-phylo] PCoA with custom distance matrix

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/

[R-sig-phylo] Problems with Bioconductor

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

Re: [R-sig-phylo] PCoA with custom distance matrix

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

Re: [R-sig-phylo] PCoA with custom distance matrix

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

[R-sig-phylo] Problems with bootstraps of NJ tree from SSRs data

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

Re: [R-sig-phylo] Problems with bootstraps of NJ tree from SSRs data

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

Re: [R-sig-phylo] Problems with bootstraps of NJ tree from SSRs data

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

Re: [R-sig-phylo] Problems with bootstraps of NJ tree from SSRs data

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

[R-sig-phylo] Probably silly question about maps

" 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

Re: [R-sig-phylo] Probably silly question about maps

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

Re: [R-sig-phylo] Probably silly question about maps

- 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

Re: [R-sig-phylo] Problems with bootstraps of NJ tree from SSRs data

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): >

[R-sig-phylo] Triploid microsatellites?

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

Re: [R-sig-phylo] Triploid microsatellites?

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.

Re: [R-sig-phylo] Triploid microsatellites?

="/" 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:

Re: [R-sig-phylo] Triploid microsatellites?

, 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

Re: [R-sig-phylo] Triploid microsatellites?

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

Re: [R-sig-phylo] Triploid microsatellites?

.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]

Re: [R-sig-phylo] Triploid microsatellites?

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

Re: [R-sig-phylo] Triploid microsatellites?

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

Re: [R-sig-phylo] Triploid microsatellites?

; 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

Re: [R-sig-phylo] Pegas Tajimas Test

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

Re: [R-sig-phylo] [adegenet-forum] Not working Monmonier

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

Re: [R-sig-phylo] [adegenet-forum] Not working Monmonier

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

Re: [R-sig-phylo] Antw: Re: [adegenet-forum] Isolation by distance (Mantel test)

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

[R-sig-phylo] Network from gene trees

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

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

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

[R-sig-phylo] Replacement of Phybase - species tree from gene trees

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

Re: [R-sig-phylo] Replacement of Phybase - species tree from gene trees

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

Re: [R-sig-phylo] Replacement of Phybase - species tree from gene trees

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 > > &

Re: [R-sig-phylo] Replacement of Phybase - species tree from gene trees

; 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

Re: [R-sig-phylo] Replacement of Phybase - species tree from gene trees

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

[R-sig-phylo] Failing chronos - how to find problem?

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

Re: [R-sig-phylo] Failing chronos - how to find problem?

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

Re: [R-sig-phylo] Phylogenetic PCA

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/

Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus

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/

Re: [R-sig-phylo] Help-forcing monophyly of outgroups and PP values of consensus

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

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

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

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

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

[R-sig-phylo] Problem with bootstraping microstallite NJ tree

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

Re: [R-sig-phylo] Problem with bootstraping microstallite NJ tree

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

Re: [R-sig-phylo] continued maintenance of the R-Phylo wiki

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

Re: [R-sig-phylo] continued maintenance of the R-Phylo wiki

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

Re: [R-sig-phylo] Query about Phylogenetics in R

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,

Re: [R-sig-phylo] Query about Phylogenetics in R

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/

Re: [R-sig-phylo] error when using function read.GenBank in ape

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] > >>>

Re: [R-sig-phylo] error when using function read.GenBank in ape

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, >

Re: [R-sig-phylo] error when using function read.GenBank in ape

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

[R-sig-phylo] Graphically comparing multiple trees

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

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

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

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

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

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

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

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

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 > >

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

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

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

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

[R-sig-phylo] Removing columns containing "N" in DNA alignment

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.

Re: [R-sig-phylo] Removing columns containing "N" in DNA alignment

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

Re: [R-sig-phylo] Removing columns containing "N" in DNA alignment

.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: > &

Re: [R-sig-phylo] Removing columns containing "N" in DNA alignment

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 &

Re: [R-sig-phylo] Removing columns containing "N" in DNA alignment

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

[R-sig-phylo] Branch lengths in phytools::plot.cophylo

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

Re: [R-sig-phylo] Branch lengths in phytools::plot.cophylo

#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

Re: [R-sig-phylo] Branch lengths in phytools::plot.cophylo

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()

[R-sig-phylo] Trimming protein alignment

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

Re: [R-sig-phylo] Trimming protein alignment

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&

Re: [R-sig-phylo] Trimming protein alignment

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

Re: [R-sig-phylo] Trimming protein alignment

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

[R-sig-phylo] ape::muscle doesn't work with Muscle5

;) : 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

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

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

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

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

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

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

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

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

[R-sig-phylo] kdetrees

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