Introduction
This is a subquadratic algorithm for detecting backbone sequences that are discordant with a given input phylogeny. A usecase is when the input tree is computed using a seperate set of biological sequences on the same set of species. More concretely, the input tree can be species tree inferred using many genes and input alignment can be a single gene.
The algorithm is subquatratic with respect to the number of species thanks to APPLES-2.
Usage
The first input is a multiple sequence alignment. The second input is a phylogenetic tree whose leaves are the input alignments. The third argument is nuc for nucleotide and prot for protein.
Examples:
For nucleotide alignment:
FastLoo aln.fa backbone.nwk nuc
For protein alignment:
FastLoo aln.fa backbone.nwk prot
You can test the tool by running the following command
FastLoo data/ref.fa data/backbone.nwk nuc
Installation:
run install.sh and then activate the conda environment conda activate fastloo