I have noticed that in ape 3.0-7, read.dna on Linux does not parse fasta
files with Windows line endings (i.e. CRLF \r\n). It results in the
addition of "\r" to the taxon label, e.g. "taxonA\r" rather than the
behaviour of 3.0-6, which was "taxonA".
Hope this makes sense, and thanks for any explan
Dear Gian,
Have you looked at the "spider" package? Sequences can be downloaded from
the GenBank or BOLD databases, and OTUs can then be estimated from a
distance matrix using a predefined threshold ("tclust" function), or by a
threshold estimated from the data ("localMinima" function).
If you wa
I have noticed that in ape 3.0-8, read.dna on Linux ignores the
"comment.char" argument, either as the default "#", or any other character.
Rupert
#Here's an MWE.
##
zz <- file("test.fas", "w")
cat(">taxonA#comment", "actg", ">taxonB#comment", "actt",
">taxonC#comment", "aatt", file = zz, sep =
I was unable to install Biostrings using my R GUI (RKWard for Ubuntu), so
this may help if anyone runs into the same problem as me ...
I was getting the error "Error in `row.names<-.data.frame`(`*tmp*`, value =
aa) : duplicate 'row.names' are not allowed".
This appeared to be a GUI specific error
Dear Pedro,
Take a look at the 'spider' package in R. There are several functions for
these kind of analyses with distances, particularly 'sppDistMatrix()'.
Cheers
On 19 February 2016 at 11:00, wrote:
> Re: Pairwise Distances
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___
Just a quick note to announce that the `spider` package is once again
available on CRAN (v1.5.0).
`Spider` is mainly aimed at DNA barcoding, but has a wide range of
functions for DNA and tree data that might be of interest more generally.
We've also moved the codebase to GitHub, and are keen to e
