AleRax: interpretation of the output of HGT highways inference

[Jason Wayne]

Dear Dr. Benoit

I hope this finds you well!

When attempting to infer horizontal gene transfer (HGT) highways, I used the following command:

alerax -f  CONFIGURATION -s random -p PREFIX  --highways

The output directory labeled "highways" includes a subdirectory called "families" with various "families_highway_" files, a text document named "highway_accepted_highways.txt," and a series of "transferll_" files. While these outputs are undoubtedly rich in information, I have found it challenging to interpret their contents fully without more detailed explanations.

I am writing to kindly request whether it might be possible to add some explanatory notes regarding these specific output files to the AleRax wiki page that could help clarify their significance and how best to interpret them. 

I am confident that such an addition would greatly benefit not only my understanding but also that of other researchers who are utilizing AleRax in their work.

[Noah Wahl]

Hi!

Yes, this is a good idea. The highway inference is still in active development and things might change a bit but the meaning of these output files should remain similar. I will add some information about the current state to the wiki.

Best,

Noah Wahl