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 Open-Source ultimaker ultimaker (Ultimaker) / debian-backup Project
A certifiably-awesome open-source package repository curated by Ultimaker, hosted by Cloudsmith.
Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).

Debian logo prank  0.0.170427+dfsg-2

One-liner (summary)

Probabilistic Alignment Kit for DNA, codon and amino-acid sequences

Description

PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It's based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

PRANK is a command-line program for UNIX-style environments but the same sequence alignment engine is implemented in the graphical program PRANKSTER. In addition to providing a user-friendly interface to those not familiar with Unix systems, PRANKSTER is an alignment browser for alignments saved in the HSAML format. The novel format allows for storing all the information generated by the aligner and the alignment browser is a convenient way to analyse and manipulate the data.

PRANK aims at an evolutionarily correct sequence alignment and often the result looks different from ones generated with other alignment methods. There are, however, cases where the different look is caused by violations of the method's assumptions. To understand why things may go wrong and how to avoid that, read this explanation of differences between PRANK and traditional progressive alignment methods.

License

Unknown

Size

316.5 KB

Downloads

0

Status  Completed
Checksum (MD5) 1305335a988324d6a07328157ec4d192
Checksum (SHA-1) 1d4d4378ad8728ec35385b9cbdb8dad439e2fff8
Checksum (SHA-256) 0c197b854b0f34f5fda02c23e48a1555f578ca49477efaec7d5e5c4669f2838d
Checksum (SHA-512) af4597d8f9bbabdd42687246d063db24c395b48ecff632778c60cbad41a4c7b664…
GPG Signature
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 3 months, 1 week ago
Uploaded By alex-borro
Slug Id prank_00170427dfsg-2_arm64deb-dzjm
Unique Id yh3A1OYyJEEx
Version (Raw) 0.0.170427+dfsg-2
Version (Parsed)
  • Major: 0
  • Minor: 0
  • Patch: 170427
  • Type: SemVer (Strict)
  • Metadata: dfsg-2
  extended metadata
Homepage http://wasabiapp.org/software/prank/
Installed Size 993.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section science
pkg prank_0.0.170427+dfsg-2_arm64.d… 0
316.5 KB
md5 sha1 sha256 sha512
Package Contents (prank_0.0.170427+dfsg-2_arm64.deb)
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This package has 17 files/directories.

Dependencies

4

Checksum (md5)

04d078f037febf5cfa71ee4e2e3fcddd

Depends
libc6 >=2.27
Depends
libgcc1 >=1:3.0
Depends
libstdc++6 >=5.2
Enhances
t-coffee

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<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/prank/0.0.170427+dfsg-2/a=arm64;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/prank/0.0.170427+dfsg-2/a=arm64;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 'prank' @ Cloudsmith" /></a>

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rendered as: Latest version of 'prank' @ Cloudsmith

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

To install/use prank @ version 0.0.170427+dfsg-2 ...

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 prank=0.0.170427+dfsg-2
Warning: Note that this package is for Debian 10 (Buster) / arm64 and may only work for that configuration.
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