Phylogenetic Analysis Workflows - User-Level Workflow Design: A Bioinformatics Perspective - page 77

Tabl e 3.1 Selection of services from the EMBOSS domain model
Service Input types Output types
degapseq Sequence record Sequence record
edialign Sequence record Sequence alignment ,
Sequence record
ehmmbuild Sequence record (protein) Hidden Markov Model ,
Sequence alignment (protein)

ehmmemit Hidden Markov Model Sequence record (protein)

Phylogenetic tree ,
Sequence record

Sequence record

emma

Phylogenetic tree ,
Sequence record

eomega Sequence record

Sequence record ,

Phylogenetic tree ,

eomegash Sequence-profile

Sequence record

alignment (HMM)

Phylogenetic tree ,

Sequence record ,

eomegasp Sequence record ,

Sequence distance matrix

Sequence-profile

fconsense Phylogenetic tree Phylogenetic tree

Sequence record

fdnacomp Phylogenetic tree

(nucleic acid)

Sequence alignment

fdnaml Phylogenetic tree

(nucleic acid)

Sequence alignment

fdnapars Phylogenetic tree

(nucleic acid)

Sequence alignment

fdnapenny Phylogenetic tree

(nucleic acid)
fdrawgram Phylogenetic tree Phylogenetic tree

fdrawtree Phylogenetic tree Phylogenetic tree

Sequence alignment

fproml Phylogenetic tree

(protein)

Sequence alignment

fprotpars Phylogenetic tree

(protein)

Phylogenetic report
(tree distances)

ftreedist Phylogenetic tree

Sequence record

makenucseq -

makeprotseq - Sequence record (protein)

revseq Sequence record Sequence record (nucleic acid)

Sequence record Sequence record (protein)

transeq

trimseq Sequence record Sequence record