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 Open-Source — ultimaker ultimaker (Ultimaker) / debian-backup — Project
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Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).
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Debian logo mptp  0.2.4-1

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One-liner (summary)

single-locus species delimitation

Description

Implementation of a fast species delimitation method, based on PTP (Zhang et al. 2013) with a 64-bit multi-threaded design that handles very large datasets.

The tool mPTP can handle very large biodiversity datasets. It implements a fast method to compute the ML delimitation from an inferred phylogenetic tree of the samples. Using MCMC, it also computes the support values for each clade, which can be used to assess the confidence of the ML delimitation.

ML delimitation mPTP implements two flavours of the point-estimate solution. First, it implements the original method from (Zhang et al. 2013) where all within-species processes are modelled with a single exponential distribution. mPTP uses a dynamic programming implementation which estimates the ML delimitation faster and more accurately than the original PTP. The dynamic programming implementation has similar properties as (Gulek et al. 2010). See the wiki for more information. The second method assumes a distinct exponential distribution for the branching events of each of the delimited species allowing it to fit to a wider range of empirical datasets.

MCMC method mPTP generates support values for each clades. They represent the ratio of the number of samples for which a particular node was in the between-species process, to the total number of samples.

License

Unknown

Size

54.8 KB

Downloads

0

Tags

debian/buster deb armhf main latest

Status  Completed
Checksum (MD5) 9b7e7cc04d21e7a285e82f6a691f7d49
Checksum (SHA-1) d4f7c454bda11a5491b83ea5e4dd1a2bb360ecc4
Checksum (SHA-256) 3d806d9db9ba01b396c3fcb81cd983b6c2d4fff488a34069aea973456f1b0fee
Checksum (SHA-512) 9987b11d9a3dca4b698bf549b36228332b32ccaadc6a6ebeae9d5ed0182cc1a499…
GPG Signature
Download
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 5 months, 2 weeks ago
Uploaded By alex-borro
Slug Id mptp_024-1_armhfdeb-krz2
Unique Id J05F4p2tVZOG
Version (Raw) 0.2.4-1
Version (Parsed)
  • Major: 0
  • Minor: 2
  • Patch: 4
  • Pre (Str): (empty)
  • Pre (Num Array): 1
  • Type: SemVer (Strict)
  extended metadata
Homepage https://github.com/Pas-Kapli/mptp
Installed Size 131.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
pkg mptp_0.2.4-1_armhf.deb 0
54.8 KB 		md5 sha1 sha256 sha512
Package Contents (mptp_0.2.4-1_armhf.deb)
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This package has 17 files/directories.

Dependencies

4

Checksum (md5)

9df3149c8b7b804541512235ede1f352

Depends
libc6 >=2.8
Depends
libgsl23
Depends
libgslcblas0
Recommends
bash-completion
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rendered as: Latest version of 'mptp' @ Cloudsmith

These instructions assume you have setup the repository first (or read it).

To install/use mptp @ version 0.2.4-1 ...

To install packages, you can quickly setup the repository automatically (recommended): 

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E bash

If you need to force a specific distribution, release/version, architecture, or component (if supported), you can also do that (e.g. if your system is compatible but not identical): 

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E distro=debian codename=buster arch=ARCH component=COMPONENT bash

or ... you can manually configure it yourself before installing packages: 

apt-get install -y debian-keyring  # debian only
apt-get install -y debian-archive-keyring  # debian only
apt-get install -y apt-transport-https
# For Debian Stretch, Ubuntu 16.04 and later
keyring_location=/usr/share/keyrings/ultimaker-debian-backup-archive-keyring.gpg
# For Debian Jessie, Ubuntu 15.10 and earlier
keyring_location=/etc/apt/trusted.gpg.d/ultimaker-debian-backup.gpg
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/gpg.C334EFCB2C4F9BE3.key' |  gpg --dearmor >> ${keyring_location}
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/config.deb.txt?distro=debian&codename=buster&component=main' > /etc/apt/sources.list.d/ultimaker-debian-backup.list
sudo chmod 644 ${keyring_location}
sudo chmod 644 /etc/apt/sources.list.d/ultimaker-debian-backup.list
apt-get update
sudo apt-get install mptp=0.2.4-1
Warning: Note that this package is for Debian 10 (Buster) / armhf and may only work for that configuration.
Still stuck? Need help? Don't panic. Just contact us for help (even if you're not a customer).
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