The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
The main purpose of delimtools
is to provide helper
functions for analyzing single locus species delimitation outputs. To
generate this type of data, it is necessary to install third-party
software and use the appropriate *_tbl()
functions to parse
these results in a tabular format.
Function | Software | Language | Source |
---|---|---|---|
abgd_tbl() | ABGD | C | https://bioinfo.mnhn.fr/abi/public/abgd/abgdweb.html |
asap_tbl() | ASAP | C | https://bioinfo.mnhn.fr/abi/public/asap/ |
bgmyc_tbl() | bGMYC | R | https://nreid.github.io/software/ |
gmyc_tbl() | splits | R | https://splits.r-forge.r-project.org/ |
locmin_tbl() | spider | R | https://github.com/boopsboops/spider |
mptp_tbl() | mptp | C | https://github.com/Pas-Kapli/mptp |
Although some of the listed software above are written using R
language, only the spider
package is available on CRAN, and
its installation is straightforward:
The splits
package can be installed using R-Forge
repository. Set dependencies = TRUE
to install
paran
package.
Although the bGMYC
package can be installed from Noah
Reid’s GitHub page, we recommend installing it from our drat repository since our
version is stable when using R >= 4.x.x
. When running
the “older” bGMYC
version using R >= 4.x.x
,
all tips of the ultrametric tree are classified as distinct lineages.
Thus, install the “stable” version by using devtools
or by
downloading the tarball and installing it manually:
The instructions below are to compile ABGD
,
ASAP
, and mPTP
in Unix systems. If you are a
Windows user, you can try to use a C compiler to create executable files
for these software but we do not guarantee it will work as intended.
Alternativelly, you may use the currently available Web servers of these
software to generate results and import them using its respective
*_tbl()
functions.
To install ABGD
, download latest release, decompress and
compile. Optionally, you may add the folder to your PATH environment
variable or move it to /usr/local/bin
.
To install ASAP
, download latest release, decompress and
compile. Optionally, you may add the folder to your PATH environment
variable or move it to /usr/local/bin
.
To install mPTP
, you can check mPTP repository and follow
their instructions.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.