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ekmolloy / treemerge

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Merge two trees with no shared nodes #1

Open magibc opened 2 years ago

magibc commented 2 years ago

Dear @ekmolloy

I'm posting here because from your research article I think that perhaps could not be possible but I prefer to ask here to be sure. Thanks on advance.

I'm trying to construct an unique phylogenetic tree containing Archaea and Bacteria for using as phyloseq object and to calculate beta-diversity Unifrac in a metagenomic study.

However, the database used (UHGG) has been used GTDB-TK software that the protein alignments and trees are splitted to separate Archaea and Bacteria files.

Could MergeTree perform the DTM method from two independent binary trees and two independent MSA files that not shared any species identifier?

The crude files are available on: http://ftp.ebi.ac.uk/pub/databases/metagenomics/mgnify_genomes/human-gut/v1.0/phylogenies/

Thanks on advance for your reply,

Magí.

ekmolloy commented 2 years ago

This specific algorithm / code base needs auxiliary information (MSA, dissimilarity matrix, etc) on the full species set in order to combine trees on pairwise disjoint species sets. I could modify the code to work if for the case where you have limited shared information (e.g. a dissimilarity matrix or MSA for a subset of species of species in tree 1 and a subset of species in tree 2), although this could lead to issues with phylogenetic terraces. Let me know if you want to discuss further! (email: ekmolloy@umd.edu)

magibc commented 2 years ago

Dear @ekmolloy,

Thanks for your rapid reply.

I have a MSA file for all species in both trees. Due to I have used the last version of UHGG database, and I constructed the new trees through IQTREE, which I have some confident data, I prefer to send you an e-mail with a link to download. My email is dbarsatidibell.cat

Thanks on advance. I write during today.

David.