[Enhancement] AliSim input/output without files

[AlinaLeu]

Hello

I would like to use AliSim within a python script where I first generate Newick strings, generate alignments from these trees using AliSim and then post-process these alignments.
Currently, (if I didn't miss something) I need to save my generated Newick strings in a tree file before using AliSim and afterwards I need to read the alignments from AliSim's output files.

It would be really helpful, if also Newick strings instead of tree files can be given as input to AliSim and if there would be an option to print the output to stdout instead of saving it to a file.

Thanks!
Alina

[trongnhanuit]

Dear Alina,

Thank you for using AliSim!

That's a great suggestion! We'll consider it for the new releases of AliSim.

Besides, AliSim can simulate alignments from a randomly generated tree (under biologically plausible processes such as Yule-Harding, and Birth-Death; and the branch lengths are generated from exponential (default) or user-specified distributions, for more details, pls see Manuals). If that feature could meet your requirements for the input trees, then it could help to save the first step in your aforementioned workflow.

Cheers,
Nhan

[AlinaLeu]

Dear Nhan

Great! And thanks for the information about the feature, this could indeed be very helpful.

Best,
Alina

[bqminh]

Is this feature already implemented?

[trongnhanuit]

Hi all,
I haven't implemented this feature yet. Due to limited time, we'll prioritize new feature requests based on user interest. If we see more interest from potential users (e.g., via thumbs up on the original post, additional comments, etc.), we'll consider implementing it. Thank you for your understanding!