-
Notifications
You must be signed in to change notification settings - Fork 63
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Generate distance matrix rather than pairwise #5
Comments
Yes, this should be easy, will add it soon. Thanks for the feedback. |
Assuming you haven't already done this, it should be output as a PHYLIP distance matrix. These can be in lower triangle form, or full matrix. For full matrix, they need to be symetrical, so you will need to average A vs B and B vs A as fastANI is not symmetric? For lower triangle, just use whatever is in query? The PHYLIP format is:
|
Yes thanks. Miguel, who is co-author of FastANI also pointed me to PHYLIP format for this purpose. I hope to add this soon, along with multi-threaded execution feature. |
Looking forward to it ! |
Hi, option to output matrix is available in the latest version; please check when you get chance. |
@cjain7 is the matrix the default output now? or is there a command line option? I can't see "matrix" anywhere in the README. |
@tseemann Looks like it is now a command line option |
@fmaguire is right. I've added this info to README now. Thanks! |
Hi, is it possible to reopen this issue to include a redundant matrix? Or could anyone provide a suggestion on how to transform the lower triangular which is outputted as a redundant/upper triangular? Thank you for any assistance you can provide. |
@vinisalazar Optionally, if you are familiar with C/C++, you can modify the source code; in particular the last ten or so instructions of the function |
So I thought, but I really could not find a tested function/library to do so. Thank you for the help regardless. |
Would it be possible to add an option to output a distance matrix in TSV or CSV instead of the pairwise list?
It could be upper triangle, lower triangle, or both.
The text was updated successfully, but these errors were encountered: