search

tahiri-lab / aPhyloGeo

aPhyloGeo is a multiplatform application for the analysis of genetic and climatic conditions.
https://pypi.org/project/aphylogeo/
GNU General Public License v3.0
10 stars 6 forks source link

Add example usage with step-by-step instructions #40

Closed annazhukova closed 3 months ago

annazhukova commented 4 months ago

Currently I have found a Getting Started web page that gives some information on the pipeline use. Having an explicit step-by-step example with data provided in the github and commands stated would be very helpful to start using the software and understand how it is expected to work

hazem-dev commented 3 months ago

Thank you for bringing this to our attention. We have taken steps to improve the documentation and user support for our software. Specifically, we have updated the wiki to offer a more detailed and clear explanation of the software's functionality. This should help users understand the capabilities and features more comprehensively.

Furthermore, we have added a thorough tutorial designed to guide users through the analysis process step-by-step. This tutorial includes detailed instructions and examples to ensure that users can effectively utilize the software for their specific needs.

annazhukova commented 3 months ago

Thank you for the tutorial, it is really nice and I could reproduce the steps !

There seems to be a little problem in the beginning:

It starts like...

We selected only 5 of 38 lineages with regional characteristics for further study (see Koshkarov et al., 2022).

There seems to be a bit of context missing. I am not sure what are those 38 lineages.

As shown in Figure 2...

I am not sure where to look for the Figure 2

And also it would be really great if you could add a few words on how to interpret the results obtained by the pipeline, "geneticTrees.json" for example.

hazem-dev commented 3 months ago

Thank you, @annazhukova. Your feedback was instrumental in identifying areas for improvement in our documentation. We have updated the wiki to provide clearer context regarding the selection of the 5 lineages from the original 38 and to offer detailed guidance on interpreting the "geneticTrees.json" file. These revisions significantly enhance the clarity and usability of our GitHub repository's wiki.