Package: metaphlan2 (3.0.14-1)

Links for metaphlan2

Trisquel Resources:

Download Source Package metaphlan2:

Maintainer:

Debian Med Packaging Team (Mail Archive)

Original Maintainers:

Debian Med Packaging Team (Mail Archive)
Andreas Tille

External Resources:

Homepage [bitbucket.org]

Similar packages:

Metagenomic Phylogenetic Analysis

MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. From version 2.0, MetaPhlAn is also able to identify specific strains (in the not-so-frequent cases in which the sample contains a previously sequenced strains) and to track strains across samples for all species.

MetaPhlAn 2.0 relies on ~1M unique clade-specific marker genes (the marker information file can be found at usr/share/metaphlan2/utils/markers_info.txt.bz2) identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic), allowing:

 * unambiguous taxonomic assignments;
 * accurate estimation of organismal relative abundance;
 * species-level resolution for bacteria, archaea, eukaryotes and
   viruses;
 * strain identification and tracking
 * orders of magnitude speedups compared to existing methods.
 * metagenomic strain-level population genomics

Other Packages Related to metaphlan2

depends

recommends

suggests

dep: bowtie2

ultrafast memory-efficient short read aligner
dep: metaphlan2-data

data package for Metagenomic Phylogenetic Analysis
dep: python3

interactive high-level object-oriented language (default python3 version)
dep: python3-biom-format

Biological Observation Matrix (BIOM) format (Python 3)
dep: python3-biopython

Python3 library for bioinformatics
dep: python3-dendropy

DendroPy Phylogenetic Computing Library (Python 3)
dep: python3-h5py-serial

general-purpose Python interface to hdf5 (Python 3 serial)
dep: python3-msgpack

Python 3 implementation of MessagePack format
dep: python3-numpy

Fast array facility to the Python 3 language
dep: python3-pandas

data structures for "relational" or "labeled" data
dep: python3-pysam

interface for the SAM/BAM sequence alignment and mapping format (Python 3)
dep: python3-requests

elegant and simple HTTP library for Python3, built for human beings
dep: python3-scipy

scientific tools for Python 3

Download metaphlan2

Download for all available architectures
Architecture	Package Size	Installed Size	Files
all	664.4 kB	2427 kB	[list of files]

Sections