Predict recomination events in bacterial genomes
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
newick:file
A Newick formatted tree based on multiple sequence alignment
*.{newick,treefile,dnd}
msa:file
A multiple sequence alignment in FASTA format
*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}
emsim
*.emsim.txt:file
Bootstrapped values for the three parameters R/theta, nu and delta
*.emsim.txt
em
*.em.txt:file
Point estimates for R/theta, nu, delta and the branch lengths
*.em.txt
status
*.importation_status.txt:file
List of reconstructed recombination events
*.importation_status.txt
newick
*.labelled_tree.newick:file
Tree with all nodes labelled
*.labelled_tree.newick
fasta
*.ML_sequence.fasta:file
Sequence reconstructed by maximum likelihood
*.ML_sequence.fasta
pos_ref
*.position_cross_reference.txt:file
CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta
*.position_cross_reference.txt
versions
versions.yml:file
File containing software versions
versions.yml
Efficient inferencing of recombination in bacterial genomes
