Giters

emmanuelparadis / ape

analysis of phylogenetics and evolution

Home Page:http://ape-package.ird.fr/

Geek Repo:Geek Repo

Github PK Tool:Github PK Tool

Cannot compute distance

fullertonhe opened this issue · comments

commented

I have an ape generated tree for ASV data, but when I try to calculate the distance, it fails with "Error in dist.nodes(x) : tree too big"

commented

There is a hard limit for computing the total cophenetic matrix of a tree. This limit applies to the number of tips + number of (internal) nodes and is set to 46,340. It's not possible to go beyond this limit without modifying the internal code (and recompiling/installing ape).
How big is your tree?

commented

I've improved the internal code so that there is no more this limit. But dist.nodes builds a square matrix which will require a lot of memory with big trees. This new code has been pushed on GH.