Cloudsmith - Repositories - Ultimaker (ultimaker) - debian-backup (debian-backup) - t-coffee

Package Search Help

You can use boolean logic (e.g. AND/OR/NOT) for complex search queries. For more help and examples, see the search documentation.

Search by package name:
my-package _(implicit)
name:my-package _(explicit)

Search by package filename:
filename:my-package.ext

Search by package tag:
tag:latest

Search by package version:
version:1.0.0 prerelease:true _{(prereleases)}
prerelease:false _{(no prereleases)}

Search by package architecture:
architecture:x86_64

Search by package distribution:
distribution:el

Search by package license:
license:MIT

Search by package format:
format:deb

Search by package status:
status:in_progress

Search by package file checksum:
checksum:5afba

Search by package security status:
severity:critical

Search by package vulnerabilities:
vulnerabilities:>1
vulnerabilities:<1000

Search by # of package downloads:
downloads:>8
downloads:<100

Search by package type:
type:binary
type:source

Search by package size (bytes):
size:>50000
size:<10000

Search by dependency name/version:
dependency:log4j
dependency:log4j=1.0.0
dependency:log4j>1.0.0

Search by uploaded date:
uploaded:>"1 day ago"
uploaded:<"August 14, 2022 EST"

Search by entitlement token (identifier):
entitlement:3lKPVJPosCsY

Search by policy violation:
policy_violated:true
deny_policy_violated:true
license_policy_violated:true
vulnerability_policy_violated:true

Search by repository:
repository:repo-name

Search by last download date:
last_downloaded:<"30 days ago"
last_downloaded:>"August 14, 2022 EST"

Search queries for all Debian-specific (and related) package types

Search by component:
deb_component:unstable

Search queries for all Maven-specific (and related) package types

Search by group ID:
maven_group_id:org.apache

Search queries for all Docker-specific (and related) package types

Search by image digest:
docker_image_digest:sha256:7c5..6d4
(full hashref only)

Search by layer digest:
docker_layer_digest:sha256:4c4..ae4
(full hashref only)

Search queries for all Generic-specific package types

Search by file path:
generic_filepath:path/to/file.txt

Search by directory:
generic_directory:path/to

Field type modifiers (depending on the type, you can influence behaviour)

For all queries, you can use:
~foo for negation

For string queries, you can use:
^foo to anchor to start of term
foo$ to anchor to end of term
foo*bar for fuzzy matching

For number/date or version queries, you can use:
>foo for values greater than
>=foo for values greater / equal
<foo for values less than
<=foo for values less / equal

Need a secure and centralised artifact repository to deliver Alpine, Cargo, CocoaPods, Composer, Conan, Conda, CRAN, Dart, Debian, Docker, Generic, Go, Helm, Hex, HuggingFace, LuaRocks, Maven, npm, NuGet, P2, Python, RedHat, Ruby, Swift, Terraform, Vagrant, VSX, Raw & More packages?

Cloudsmith is the new standard in Package / Artifact Management and Software Distribution.

With support for all major package formats, you can trust us to manage your software supply chain.

Start My Free Trial

Set Me Up

Open-Source — 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).

t-coffee 12.00.7fb08c2-4

Download

One-liner (summary)

Multiple Sequence Alignment

Description

T-Coffee is a multiple sequence alignment package. Given a set of sequences (Proteins or DNA), T-Coffee generates a multiple sequence alignment. Version 2.00 and higher can mix sequences and structures.

T-Coffee allows the combination of a collection of multiple/pairwise, global or local alignments into a single model. It can also estimate the level of consistency of each position within the new alignment with the rest of the alignments. See the pre-print for more information

T-Coffee has a special called M-Coffee that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer.

License

Unknown

Size

1.3 MB

Downloads

Status	Completed
Checksum (MD5)	45f3337e369ceab6f9723dcd14718452
Checksum (SHA-1)	de8a8affe5a8d6bc80dfe07be00b2149949bbadc
Checksum (SHA-256)	d956a116b4487e901f2847d4a1fc904083c5d7b6e49db8ac72d244ef50a7efde
Checksum (SHA-512)	690f15a9896409230e9e688a0193ad00186aaa10db7d2ce602ec959ac2bbb0a028…
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	1 year ago
Uploaded By
Slug Id	t-coffee_12007fb08c2-4_armhfdeb-kwkt
Unique Id	UQxRhlusLW1p
Version (Raw)	12.00.7fb08c2-4
Version (Parsed)	Major: 12 Minor: 0 Patch: 7 Type: SemVer (Compat) Extra: fb08c2-4
	extended metadata
Homepage	http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
Installed Size	6.4 MB
Maintainer	Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority	optional
Section	science

Dependencies

Checksum (md5)

6475fa81a4ea2c6f27ae83bf43272585

Depends	libc6	>=2.27
Depends	libgcc1	>=1:3.5
Depends	libstdc++6	>=4.3.0
Recommends	amap-align
Recommends	clustalo
Recommends	clustalw
Recommends	dialign-tx
Recommends	fsa
Recommends	kalign
Recommends	libsoap-lite-perl
Recommends	libxml-simple-perl
Recommends	mafft
Recommends	muscle
Recommends	mustang
Recommends	ncbi-blast+
Recommends	poa
Recommends	prank
Recommends	probcons
Recommends	proda
Recommends	tm-align
Suggests	boxshade
Suggests	seaview
Suggests	t-coffee-examples

Package statistics are no longer available on cloudsmith.io. Please visit our new web app to access this feature.

You can embed a badge in another website that shows this or the latest version of this package.

To embed the badge for this specific package version, use the following:

[![This version of 't-coffee' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/t-coffee/12.00.7fb08c2-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/t-coffee/12.00.7fb08c2-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)

|This version of 't-coffee' @ Cloudsmith|
.. |This version of 't-coffee' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/t-coffee/12.00.7fb08c2-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/t-coffee/12.00.7fb08c2-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/t-coffee/12.00.7fb08c2-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/t-coffee/12.00.7fb08c2-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="This version of 't-coffee' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/t-coffee/12.00.7fb08c2-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/t-coffee/12.00.7fb08c2-4/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true" alt="This version of 't-coffee' @ Cloudsmith" /></a>

rendered as:

To embed the badge for the latest package version, use the following:

[![Latest version of 't-coffee' @ Cloudsmith](https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/t-coffee/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true)](https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/t-coffee/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/)

|Latest version of 't-coffee' @ Cloudsmith|
.. |Latest version of 't-coffee' @ Cloudsmith| image:: https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/t-coffee/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true
   :target: https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/t-coffee/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/

image::https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/t-coffee/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true[link="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/t-coffee/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/",title="Latest version of 't-coffee' @ Cloudsmith"]

<a href="https://cloudsmith.io/~ultimaker/repos/debian-backup/packages/detail/deb/t-coffee/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/"><img src="https://api.cloudsmith.com/v1/badges/version/ultimaker/debian-backup/deb/t-coffee/latest/a=armhf;xc=main;d=debian%252Fbuster;t=binary/?render=true&show_latest=true" alt="Latest version of 't-coffee' @ Cloudsmith" /></a>

rendered as:

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

To install/use t-coffee @ version 12.00.7fb08c2-4 ...

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 t-coffee=12.00.7fb08c2-4

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).

Previous Version

Next Version