Regarding the output file.

gauri84's Avatar


03 May, 2016 08:57 AM

Hi there,

I ran the command line for Treefam in Linux and got this output file (attached here). However, I have no clue as to how to proceed from here ...I want a Multiple Sequence Alignment followed by phylogenetic tree and orthologous genes prediction. I checked online but could not find anything documented properly. Like the TreeFam windows online version gives us the complete output the Linux version is not explained properly (No proper commands given).
Would request you to guide me.


  1. Support Staff 1 Posted by Matthieu Muffat... on 04 May, 2016 05:30 PM

    Matthieu Muffato's Avatar

    Dear Gauri,

    The output in your screenshot already tells you the homologies. Indeed we don't have (yet) a standalone tool to infer the trees and the orthologies.
    If you want to build orthologies for a whole proteome, you'd currently have to get the existing alignments + trees of all the families and run tools yourselves. We'd recommend Mafft + RAxML + some custom parsing of the trees. Unfortunately all our pipelines require an infrastructure that is still difficult to setup and is not much tested outside of our own environment, so I think its cost would outweigh the burden of running things on your own


  2. Matthieu Muffato closed this discussion on 04 May, 2016 05:30 PM.

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