[R-sig-phylo] phangorn - midpoint function

Hi! I am using the function midpoint of package phangorn to root my trees (which I generated by simulations). A negative branch length is added to my tree after I use the midpoint function. The same does not happen if I use FigTree for example. Does anyone know why that happens? I cannot

[R-sig-phylo] chronos function

Hi, I am analyzing lots of trees in which I need it to be ultrametric. I decided to use the function chronos, but in the middle of my run I got the following error message which I don't know the meaning: Error in nlminb(start.para, f, g, control = opt.ctrl, lower = LOW, upper = UP) :  

[R-sig-phylo] chronos and gammaStat

Hi! I am using the gammaStat in ape to analyze some trees I generated using simulations and RaxML. After using the R code below to convert it to ultrametric tree: cal - makeChronosCalib(Tree, age.min=1) chr - chronos(Tree, lambda = 0.1, calibration = cal) gammaStat(chr) I get the following

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

: [R-sig-phylo] chronos and gammaStat Hello Frabricia, I assume your RAxML tree is not rooted. is.rooted(chr) and use the function root if chr is not rooted. Regards, Klaus On Tue, Apr 8, 2014 at 2:03 PM, Fabricia Nascimento Hi! I am using the gammaStat in ape to analyze some trees I

[R-sig-phylo] Reading sets of multiple DNA sequence alignments

Hi,   I am new to R and I am trying to read a file containing sets of multiple sequence alignments as in the example below. The difference is that for my files, each set of sequences may contain up to 50 sequences of 10,000bp each.   Example:  5 10 Seq0     ATCGTTATTA Seq1    

Re: [R-sig-phylo] Reading sets of multiple DNA sequence alignments

/03/2014 17:56, Fabricia Nascimento a écrit : Hi,   I am new to R and I am trying to read a file containing sets of multiple sequence alignments as in the example below. The difference is that for my files, each set of sequences may contain up to 50 sequences of 10,000bp each.   Example: Ã

[R-sig-phylo] tree shape - unrooted trees

Hi, I am wondering whether anyone knows about any metrics for testing networks or unrooted tree shapes. I have tried the Colless test and the Beta index in the apTreeShape in R but they appear to be not very informative for my data (although it is still a result). And I also need to have a

Re: [R-sig-phylo] apTreeshape and as.treeshape

of unresolved nodes. Sincerely Michael Blum Le 10/06/13 17:53, Fabricia Nascimento a écrit : Hi, I am trying to use the collies.test and maxlik.betasplit tests in apTreeshape R package. I have a set of DNA sequence in fasta format. I am following the steps below. 1. I construct a NJ using

[R-sig-phylo] apTreeshape and as.treeshape

Hi, I am trying to use the collies.test and maxlik.betasplit tests in apTreeshape R package. I have a set of DNA sequence in fasta format. I am following the steps below. 1. I construct a NJ using the ape R package using the nj(dist.dna(dataset). 2. After I use the as.treeshape form the