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