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