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BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
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phyloscannerR no output when only 1 window/tree is used #38

Closed damientully closed 5 years ago

damientully commented 5 years ago

Hi guys,

When only one window is analyzed with phyloscanner_analyse_trees.R no pairwise relationship summary is printed or summary plot (a pdf is printed of the tree). I realize that this makes some sense as you may generally have multiple windows across a genome but what about if you had a single small amplicon across a region. While I could separate the amplicon into smaller windows I want to maximize the phylogenetic signal so is there a way to generate those files when only one tree is given.

Thanks Damien

mdhall272 commented 5 years ago

Hi Damien,

The reason for this is that both of those outputs are summaries across multiple windows which make little sense if you only have one. You can get the exact between-host relationships for the single tree using the --allClassifications and --collapsedTrees options.

(An alternative I recommend if you are doing a final analysis is to give phyloscanner_analyse_trees.R a set of bootstraps or posterior samples constructed from your single window alignment as input. This accounts for uncertainty in a different way, and those files will appear.)

Thanks, Matthew

damientully commented 5 years ago

Hi Matthew,

Yes that what I figured but I will try those options that you suggested.

Thanks, Damien