Installing Species Delimitation Softwares

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

Install R packages

spider

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:

install.packages("spider")

splits

The splits package can be installed using R-Forge repository. Set dependencies = TRUE to install paran package.

install.packages("splits", repos = "http://R-Forge.R-project.org", dependencies = TRUE)

bGMYC

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:

install.packages("bGMYC", repos = "https://pedrosenna.github.io/drat/")

Install C softwares

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.

ABGD

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.

wget https://bioinfo.mnhn.fr/abi/public/abgd/last.tgz -O abgd.tgz
tar -xzvf abgd.tgz
cd Abgd
make
mkdir bin
mv abgd bin/abgd
cd ..

ASAP

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.

wget https://bioinfo.mnhn.fr/abi/public/asap/last.tgz
tar -xzvf last.tgz
cd ASAP
make
mkdir bin
mv asap bin/asap
cd ..

mPTP

To install mPTP, you can check mPTP repository and follow their instructions.