Error in PHYLIP and repClonalFamily

[Rongfang-Shen]

❓ Questions and Help

We have a set of listed tutorials available on the website. Hi~ I am using repClonalFamily and install the phylip, add the path to window system. However, R cannot find the phylip software. The sys.which("phylip") return nothing, but the path "H:\phylip\phylip-3.698\exe" (which the folder I put) had been added in the PATH, and can be found in Sys.getenv("PATH"). Actually, I cannot found phylip.exc under the ..\phylip-3.698\exe folder. Cannot solve it, look for help and hope for any solution.

[Alexander230]

Hello, @Rongfang-Shen!

I'm Aleksandr Popov, a developer of Immunarch package. Thank you for using our software!

I've found that Phylip for Windows names the correct executable dnapars. There is now a fix in Immunarch that adds support for it, but now it's only in development branch; it will be included in the next release. You can install immunarch from a branch with this fix using the following commands:

install.packages(c("devtools", "pkgload"))
devtools::install_github("immunomind/immunarch", ref="phylip-windows-fix")
devtools::reload(pkgload::inst("immunarch"))

Best regards, Aleksandr

[mknewline]

Hi Alexander, I came here with the same problem. I tried to run the code you wrote to fix the issue but the link to phylip-windows-fix is broken. Can you help me with this?

Many thanks Michele

[Alexander230]

Hi, @mknewline! This branch was already merged, so you can use ref="dev" instead. Soon it will be included in the next release of Immunarch.

Best regards, Aleksandr

[mknewline]

Dear @Alexander230 MANY THANKS, it is now working! Thank you for this service to the scientific community!

Michele