Allow running mPTP and auto-estimating minimum branch length at once

[lutteropp]

Currently, the user has to first run:

mptp --tree_file my_tree --output_file file_that_will_not_be_written_but_nevertheless_is_required_to_give --minbr_auto my_fasta_file

Then the user will get an output printed to the console like "Minimum branch length (--minbr) should be set to [...]".
After that, the user can run the species delimitation.

I would appreciate if auto-estimation of the minimum branch length and inferring the species could be done in one single command line call. Currently when trying this, mPTP prints "More than one command specified."

[stamatak]

I am not so sure about this, it will be more convenient, however the
users will be much less aware of what is happening ... so it's maybe
better to leave it as is for the sake of user awareness ...

alexis

On 10.04.2016 13:16, Sarah Lutteropp wrote:

Currently, the user has to first run:

mptp --tree_file my_tree --output_file
file_that_will_not_be_written_but_nevertheless_is_required_to_give
--minbr_auto my_fasta_file

Then the user will get an output printed to the console like "Minimum
branch length (--minbr) should be set to [...]".
After that, the user can run the species delimitation.

I would prefer that auto-estimation of the minimum branch length and
inferring the species can be done in one single command.

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#68

Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson

www.exelixis-lab.org

[Pas-Kapli]

I agree with Alexis. It is important that the user is fully aware this is happening.

A potential enhancement could be printing the pairs of samples that are related with branch lengths below the threshold, when a user is doing the --minbr command.