Package: sepp (4.3.10+dfsg-5)

[ Source: sepp  ]

phylogeny with ensembles of Hidden Markov Models

The tools SEPP and TIPP implementing these methods use ensembles of Hidden Markov Models (HMMs) in different ways, each focusing on a different problem.

SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.

TIPP stands for "Taxonomic Identification and Phylogenetic Profiling", and addresses the problem of taxonomic identification and abundance profiling of metagenomic data.

Other Packages Related to sepp

• dep: hmmer

  profile hidden Markov models for protein sequence analysis

• dep: libcommons-beanutils-java

  Apache Commons BeanUtils - Utility for manipulating Java beans

• dep: libcommons-collections3-java

  Apache Commons Collections - Extended Collections API for Java

• dep: libcommons-lang-java

  Commons Lang - an extension of the java.lang package

• dep: libcommons-logging-java

  common wrapper interface for several logging APIs

• dep: libgoogle-gson-java

  Converts Java objects into their JSON representation

• dep: libjenkins-json-java

  Library for transforming Java objects between XML and JSON

• dep: libjson-java

  library for transforming Java objects and XML to JSON and back again

• dep: ncbi-blast+

  next generation suite of BLAST sequence search tools

• dep: pplacer

  phylogenetic placement and downstream analysis

• dep: python3

  interactive high-level object-oriented language (default python3 version)

• dep: python3-dendropy

  DendroPy Phylogenetic Computing Library (Python 3)

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amd64	179.6 kB	551.0 kB	[list of files]