Mask multiple sequence alignments
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’ ]
unmaskedaln{:bash}
:file
multiple sequence alignment, Stockholm or other formats
*
fmask_rf{:bash}
:boolean
Flag to output optional file with final mask of non-gap RF len
fmask_all{:bash}
Flag to output optional file with final mask of full aln len
gmask_rf{:bash}
Flag to output optional file gap-based 0/1 mask of non-gap RF len
gmask_all{:bash}
Flag to output optional file gap-based 0/1 mask of full aln len
pmask_rf{:bash}
Flag to output optional file with PP-based 0/1 mask of non-gap RF len
pmask_all{:bash}
Flag to output optional file with PP-based 0/1 mask of full aln len
maskfile{:bash}
mask file, see program documentation
maskedaln{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.masked.sthlm.gz{:bash}
Masked alignment in gzipped Stockholm format
*.sthlm.gz
*.fmask-rf.gz{:bash}
File with final mask of non-gap RF len
*.fmask-rf.gz
*.fmask-all.gz{:bash}
File with final mask of full aln len
*.fmask-all.gz
*.gmask-rf.gz{:bash}
File with gap-based 0/1 mask of non-gap RF len
*.gmask-rf.gz
*.gmask-all.gz{:bash}
File with gap-based 0/1 mask of full aln len
*.gmask-all.gz
*.pmask-rf.gz{:bash}
File with PP-based 0/1 mask of non-gap RF len
*.pmask-rf.gz
*.pmask-all.gz{:bash}
File with PP-based 0/1 mask of full aln len
*.pmask-all.gz
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Biosequence analysis using profile hidden Markov models
