Login Logged in as anonymous / My BiBiServ / Logout
Search
?
Navigation
Rose
Welcome
Submission
WebService
Download
Manual
References
Reset Session

ROSE - Random-model Of Sequence Evolution

Rose implements a new probabilistic model of RNA-, DNA-, or protein-sequence evolution. The online version supports most (important) parameter from downloadable version.

This manual subdivide into 3 main parts. The supported functions, the input-/output data and arguments(parameter).

Rose (AA)

Random model of sequence evolution (AminoAcid)

Rose (DNA)

Random model of sequence evolution (NucleicAcid)

In-/Output values

OUTPUT :: AA output

Multiple AA sequence alignment in FASTA format.

OUTPUT :: DNA output

Multiple DNA sequence alignment in FASTA format.

Parameter

Name Description
Number of sequences Number of sequences
Average length Average length of sequences
Average pairwise distance Average pairwise distance
Mean substituion Mean substituion
Transition bias Transition bias
Transition/Transversion ratio Transition/Transversion ratio
Root sequence Root sequence
Seed value Seed value
Tree Tree
Mutation probability (uniform) Mutation probability distributed uniformly
Mutation probability (base) Mutation probability specified for each base. Must be a comma separted list of float values,.e.g.: [1.0,1.0,1.0,1.0] for DNA (4 bases).
Insertion probability Insertion probability (expressed as percentage)
Insertion function Insertion function. Must be a comma separted list of float values
Deletion probability Deletion probability (expressed as percentage)
Deletion function Deletion function. Must be a comma separted list of float values
Choose from leaves Choose from leaves
DNA model DNA model to be used. One of Jukes/Cantor (JC), Hasegawa/Kishino/Yano (HKY), Felsenstein 1981 (F81), Felsenstein 1984 (F84) or Kimura's two-parameter model (K2P)
© 2010 - 2024 Bielefeld BioInformatics Service | Impressum