Summary
Phylogeny
Debian Med phylogeny packages
This lists Debian packages related to phylogeny for use in life sciences.
The purpose of this compilation of packages is to have a handy subset of
from the med-bio metapackage which contains a lot more than only phylogeny
related software.
Description
For a better overview of the project's availability as a Debian package, each head row has a color code according to this scheme:
If you discover a project which looks like a good candidate for Debian Med
to you, or if you have prepared an unofficial Debian package, please do not hesitate to
send a description of that project to the Debian Med mailing list
Links to other tasks
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Debian Med Phylogeny packages
Official Debian packages with high relevance
altree
program to perform phylogeny-based association and localization analysis
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Versions of package altree |
Release | Version | Architectures |
bullseye | 1.3.1-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.3.2-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.3.2-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 1.3.2-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.3.1-2 | amd64,armel,armhf,i386 |
stretch | 1.3.1-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.3.1-7 | amd64,arm64,armhf,i386 |
Debtags of package altree: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program, shared-lib |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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ALTree was designed to perform association detection and localization of
susceptibility sites using haplotype phylogenetic trees: first, it allows the
detection of an association between a candidate gene and a disease, and second,
it enables to make hypothesis about the susceptibility loci.
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beast-mcmc
Bayesian MCMC phylogenetic inference
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Versions of package beast-mcmc |
Release | Version | Architectures |
jessie | 1.8.0-1 (contrib) | all |
buster | 1.10.4+dfsg-1 | all |
bullseye | 1.10.4+dfsg-2 | all |
bookworm | 1.10.4+dfsg-5 | all |
trixie | 1.10.4+dfsg-5 | all |
sid | 1.10.4+dfsg-5 | all |
stretch | 1.8.4+dfsg.1-1 | all |
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License: DFSG free
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BEAST is a cross-platform program for Bayesian MCMC analysis of molecular
sequences. It is entirely orientated towards rooted, time-measured
phylogenies inferred using strict or relaxed molecular clock models. It
can be used as a method of reconstructing phylogenies but is also a
framework for testing evolutionary hypotheses without conditioning on a
single tree topology. BEAST uses MCMC to average over tree space, so that
each tree is weighted proportional to its posterior probability. Included
is a simple to use user-interface program for setting up standard
analyses and a suit of programs for analysing the results.
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clustalw
global multiple nucleotide or peptide sequence alignment
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Versions of package clustalw |
Release | Version | Architectures |
trixie | 2.1+lgpl-7 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1+lgpl-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.1+lgpl-7 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.1+lgpl-6 | amd64,arm64,armhf,i386 |
stretch | 2.1+lgpl-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1+lgpl-4 | amd64,armel,armhf,i386 |
sid | 2.1+lgpl-7 | amd64,arm64,mips64el,ppc64el,riscv64,s390x |
Debtags of package clustalw: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline, text-mode |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
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License: DFSG free
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This program performs an alignment of multiple nucleotide or amino acid
sequences. It recognizes the format of input sequences and whether the
sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The output
format may be selected from in various formats for multiple alignments such as
Phylip or FASTA. Clustal W is very well accepted.
The output of Clustal W can be edited manually but preferably with an
alignment editor like SeaView or within its companion Clustal X. When building
a model from your alignment, this can be applied for improved database
searches. The Debian package hmmer creates such in form of an HMM.
The package is enhanced by the following packages:
clustalw-mpi
Please cite:
M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson and D. G. Higgins:
Clustal W and Clustal X version 2.0.
(PubMed,eprint)
Bioinformatics
23(21):2947-2948
(2007)
Topics: Sequence analysis
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clustalx
Multiple alignment of nucleic acid and protein sequences (graphical interface)
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Versions of package clustalx |
Release | Version | Architectures |
bullseye | 2.1+lgpl-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.1+lgpl-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.1+lgpl-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.1+lgpl-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.1+lgpl-3 | amd64,armel,armhf,i386 |
stretch | 2.1+lgpl-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.1+lgpl-8 | amd64,arm64,armhf,i386 |
Debtags of package clustalx: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | x11 |
role | program |
scope | utility |
uitoolkit | motif |
use | analysing, comparing, viewing |
works-with-format | plaintext |
x11 | application |
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License: DFSG free
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This package offers a GUI interface for the Clustal multiple sequence
alignment program. It provides an integrated environment for performing
multiple sequence- and profile-alignments to analyse the results.
The sequence alignment is displayed in a window on the screen.
A versatile coloring scheme has been incorporated to highlight conserved
features in the alignment. For professional presentations, one should
use the texshade LaTeX package or boxshade.
The pull-down menus at the top of the window allow you to select all the
options required for traditional multiple sequence and profile alignment.
You can cut-and-paste sequences to change the order of the alignment; you can
select a subset of sequences to be aligned; you can select a sub-range of the
alignment to be realigned and inserted back into the original alignment.
An alignment quality analysis can be performed and low-scoring segments or
exceptional residues can be highlighted.
Please cite:
M.A. Larkin, G. Blackshields, N.P. Brown, R. Chenna, P.A. McGettigan, H. McWilliam, F. Valentin, I.M. Wallace, A. Wilm, R. Lopez, J.D. Thompson, T.J. Gibson and D.G. Higgins:
Clustal W and Clustal X version 2.0.
(PubMed,eprint)
Bioinformatics
23(21):2947-2948
(2007)
Topics: Sequence analysis
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dialign
Segment-based multiple sequence alignment
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Versions of package dialign |
Release | Version | Architectures |
trixie | 2.2.1-13 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 2.2.1-7 | amd64,armel,armhf,i386 |
stretch | 2.2.1-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 2.2.1-10 | amd64,arm64,armhf,i386 |
bullseye | 2.2.1-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.2.1-11 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.2.1-13 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package dialign: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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DIALIGN2 is a command line tool to perform multiple alignment of
protein or DNA sequences. It constructs alignments from gapfree pairs
of similar segments of the sequences. This scoring scheme for
alignments is the basic difference between DIALIGN and other global or
local alignment methods. Note that DIALIGN does not employ any kind of
gap penalty.
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dialign-tx
Segment-based multiple sequence alignment
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Versions of package dialign-tx |
Release | Version | Architectures |
jessie | 1.0.2-7 | amd64,armel,armhf,i386 |
trixie | 1.0.2-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.0.2-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 1.0.2-15 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.0.2-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0.2-12 | amd64,arm64,armhf,i386 |
stretch | 1.0.2-9 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package dialign-tx: |
field | biology, biology:bioinformatics |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
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License: DFSG free
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DIALIGN-TX is a command line tool to perform multiple alignment of protein or
DNA sequences. It is a complete reimplementation of the segment-base approach
including several new improvements and heuristics that significantly enhance
the quality of the output alignments compared to DIALIGN 2.2 and DIALIGN-T.
For pairwise alignment, DIALIGN-TX uses a fragment-chaining algorithm that
favours chains of low-scoring local alignments over isolated high-scoring
fragments. For multiple alignment, DIALIGN-TX uses an improved greedy
procedure that is less sensitive to spurious local sequence similarities.
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exonerate
generic tool for pairwise sequence comparison
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Versions of package exonerate |
Release | Version | Architectures |
buster | 2.4.0-4 | amd64,arm64,armhf,i386 |
bullseye | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.2.0-6 | amd64,armel,armhf,i386 |
stretch | 2.4.0-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.4.0-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package exonerate: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | searching |
works-with-format | plaintext |
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License: DFSG free
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Exonerate allows you to align sequences using a many alignment models, using
either exhaustive dynamic programming, or a variety of heuristics. Much of
the functionality of the Wise dynamic programming suite was reimplemented in C
for better efficiency. Exonerate is an intrinsic component of the building of
the Ensembl genome databases, providing similarity scores between RNA and DNA
sequences and thus determining splice variants and coding sequences in
general.
An In-silico PCR Experiment Simulation System (see the ipcress man page) is
packaged with exonerate.
This package also comes with a selection of utilities for performing
simple manipulations quickly on fasta files beyond 2Gb
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fastdnaml
Tool for construction of phylogenetic trees of DNA sequences
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Versions of package fastdnaml |
Release | Version | Architectures |
bookworm | 1.2.2-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.2.2-15 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.2-14 | amd64,arm64,armhf,i386 |
stretch | 1.2.2-11 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 1.2.2-17 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.2.2-17 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.2.2-10 | amd64,armel,armhf,i386 |
Debtags of package fastdnaml: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
(part of his PHYLIP package). Users should consult the documentation for
DNAML before using this program.
fastDNAml is an attempt to solve the same problem as DNAML, but to do so
faster and using less memory, so that larger trees and/or more bootstrap
replicates become tractable. Much of fastDNAml is merely a recoding of the
PHYLIP 3.3 DNAML program from PASCAL to C.
Note that the homepage of this program is not available any more and so
this program will probably not see any further updates.
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fasttree
phylogenetic trees from alignments of nucleotide or protein sequences
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Versions of package fasttree |
Release | Version | Architectures |
buster | 2.1.10-2 | amd64,arm64,armhf,i386 |
sid | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 2.1.11-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 2.1.7-2 | amd64,armel,armhf,i386 |
stretch | 2.1.9-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
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FastTree infers approximately-maximum-likelihood phylogenetic trees from
alignments of nucleotide or protein sequences. It handles alignments
with up to a million of sequences in a reasonable amount of time and
memory. For large alignments, FastTree is 100-1,000 times faster than
PhyML 3.0 or RAxML 7.
FastTree is more accurate than PhyML 3 with default settings, and much
more accurate than the distance-matrix methods that are traditionally
used for large alignments. FastTree uses the Jukes-Cantor or generalized
time-reversible (GTR) models of nucleotide evolution and the JTT
(Jones-Taylor-Thornton 1992) model of amino acid evolution. To account
for the varying rates of evolution across sites, FastTree uses a single
rate for each site (the "CAT" approximation). To quickly estimate the
reliability of each split in the tree, FastTree computes local support
values with the Shimodaira-Hasegawa test (these are the same as PhyML 3's
"SH-like local supports").
This package contains a single threaded version (fasttree) and a
parallel version which uses OpenMP (fasttreMP).
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figtree
graphical phylogenetic tree viewer
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Versions of package figtree |
Release | Version | Architectures |
jessie | 1.4-2 | all |
sid | 1.4.4-6 | all |
buster | 1.4.4-3 | all |
stretch | 1.4.2+dfsg-2 | all |
bullseye | 1.4.4-5 | all |
bookworm | 1.4.4-5 | all |
trixie | 1.4.4-6 | all |
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License: DFSG free
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FigTree is designed as a graphical viewer of phylogenetic trees and as
a program for producing publication-ready figures. In particular it is
designed to display summarized and annotated trees produced by BEAST.
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gmap
spliced and SNP-tolerant alignment for mRNA and short reads
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Versions of package gmap |
Release | Version | Architectures |
trixie | 2024-10-10+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
jessie | 2014-10-22-1 (non-free) | amd64 |
stretch | 2017-01-14-1 (non-free) | amd64 |
buster | 2019-01-24-1 (non-free) | amd64 |
bullseye | 2021-02-22+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
bookworm | 2021-12-17+ds-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el |
sid | 2024-10-20+ds-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64 |
Debtags of package gmap: |
field | biology, biology:bioinformatics, biology:structural |
role | program |
use | analysing |
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License: DFSG free
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This package contains the programs GMAP and GSNAP as well as
utilities to manage genome databases in GMAP/GSNAP format.
GMAP (Genomic Mapping and Alignment Program) is a tool for aligning
EST, mRNA and cDNA sequences.
GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for
aligning single-end and paired-end transcriptome reads.
Both tools can use a database of
- known splice sites and identify novel splice sites.
- known single-nucleotide polymorphisms (SNPs).
GSNAP can align bisulfite-treated DNA.
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hmmer
profile hidden Markov models for protein sequence analysis
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Versions of package hmmer |
Release | Version | Architectures |
bookworm | 3.3.2+dfsg-1 | amd64,i386 |
buster | 3.2.1+dfsg-1 | amd64,i386 |
trixie | 3.4+dfsg-2 | amd64,arm64,i386 |
bullseye | 3.3.2+dfsg-1 | amd64,i386 |
sid | 3.4+dfsg-2 | amd64,arm64,i386 |
jessie | 3.1b1-3 | amd64,armel,armhf,i386 |
stretch | 3.1b2+dfsg-5 | amd64,i386 |
Debtags of package hmmer: |
biology | format:aln, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | searching |
works-with | db |
works-with-format | plaintext |
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License: DFSG free
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HMMER is an implementation of profile hidden Markov model methods for
sensitive searches of biological sequence databases using multiple sequence
alignments as queries.
Given a multiple sequence alignment as input, HMMER builds a statistical
model called a "hidden Markov model" which can then be used as a query into
a sequence database to find (and/or align) additional homologues of the
sequence family.
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iqtree
efficient phylogenetic software by maximum likelihood
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Versions of package iqtree |
Release | Version | Architectures |
sid | 2.0.7+dfsg-1 | amd64,i386 |
stretch | 1.5.3+dfsg-2 | amd64,i386 |
buster | 1.6.9+dfsg-1 | amd64,i386 |
bullseye | 1.6.12+dfsg-1 | amd64,i386 |
bookworm | 2.0.7+dfsg-1 | amd64,i386 |
trixie | 2.0.7+dfsg-1 | amd64,i386 |
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License: DFSG free
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IQ-TREE is a very efficient maximum likelihood phylogenetic software
with following key features among others:
- A novel fast and effective stochastic algorithm to estimate maximum
likelihood trees. IQ-TREE outperforms both RAxML and PhyML in terms
of likelihood while requiring similar amount of computing time (see
Nguyen et al., 2015)
- An ultrafast bootstrap approximation to assess branch supports (see
Minh et al., 2013).
- A wide range of substitution models for binary, DNA, protein, codon,
and morphological alignments.
- Ultrafast model selection for all data types, 10 to 100 times faster
than jModelTest and ProtTest.
- Finding best partition scheme like PartitionFinder.
- Partitioned models with mixed data types for phylogenomic (multi-
gene) alignments, allowing for separate, proportional, or joint
branch lengths among genes.
- Supporting the phylogenetic likelihod library (PLL) (see Flouri et
al., 2014)
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jmodeltest
HPC selection of models of nucleotide substitution
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Versions of package jmodeltest |
Release | Version | Architectures |
stretch | 2.1.10+dfsg-5 | all |
sid | 2.1.10+dfsg-12 | all |
trixie | 2.1.10+dfsg-12 | all |
bullseye | 2.1.10+dfsg-10 | all |
bookworm | 2.1.10+dfsg-12 | all |
buster | 2.1.10+dfsg-7 | all |
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License: DFSG free
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jModelTest is a tool to carry out statistical selection of best-fit
models of nucleotide substitution. It implements five different model
selection strategies: hierarchical and dynamical likelihood ratio tests
(hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC),
and a decision theory method (DT). It also provides estimates of model
selection uncertainty, parameter importances and model-averaged
parameter estimates, including model-averaged tree topologies.
jModelTest 2 includes High Performance Computing (HPC) capabilities and
additional features like new strategies for tree optimization, model-
averaged phylogenetic trees (both topology and branch length), heuristic
filtering and automatic logging of user activity.
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kalign
Global and progressive multiple sequence alignment
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Versions of package kalign |
Release | Version | Architectures |
sid | 3.4.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 3.3-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.4.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.3.5-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.03+20110620-5 | amd64,arm64,armhf,i386 |
stretch | 2.03+20110620-3 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.03+20110620-2 | amd64,armel,armhf,i386 |
Debtags of package kalign: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
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License: DFSG free
|
Kalign is a command line tool to perform multiple alignment of
biological sequences. It employs the Muth-Manber string-matching
algorithm, to improve both the accuracy and speed of the alignment.
It uses global, progressive alignment approach, enriched by employing
an approximate string-matching algorithm to calculate sequence
distances and by incorporating local matches into the otherwise global
alignment.
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mrbayes
Bayesian Inference of Phylogeny
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Versions of package mrbayes |
Release | Version | Architectures |
sid | 3.2.7a-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 3.2.6+dfsg-1 | amd64,arm64,armhf,i386 |
buster | 3.2.6+dfsg-2 | amd64,arm64,armhf,i386 |
bullseye | 3.2.7a-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 3.2.7a-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.2.7a-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.2.3+dfsg-1 | amd64,armel,armhf,i386 |
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License: DFSG free
|
Bayesian inference of phylogeny is based upon a quantity called the posterior
probability distribution of trees, which is the probability of a tree
conditioned on the observations. The conditioning is accomplished using
Bayes's theorem. The posterior probability distribution of trees is
impossible to calculate analytically; instead, MrBayes uses a simulation
technique called Markov chain Monte Carlo (or MCMC) to approximate the
posterior probabilities of trees.
The package is enhanced by the following packages:
mrbayes-doc
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muscle
Multiple alignment program of protein sequences
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Versions of package muscle |
Release | Version | Architectures |
jessie | 3.8.31-1 | amd64,armel,armhf,i386 |
trixie | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 3.8.31+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.8.1551-2 | amd64,arm64,armhf,i386 |
bullseye | 3.8.1551-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.1.0-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
upstream | 5.2 |
Debtags of package muscle: |
biology | format:aln, nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
|
License: DFSG free
|
MUSCLE is a multiple alignment program for protein sequences. MUSCLE
stands for multiple sequence comparison by log-expectation. In the
authors tests, MUSCLE achieved the highest scores of all tested
programs on several alignment accuracy benchmarks, and is also one of
the fastest programs out there.
Muscle v5 is a major re-write of MUSCLE based on new algorithms.
Users should be aware that command line arguments compared to version
3.x of MUSCLE have changed!
Highest accuracy, scalable to thousands of sequences
Compared to previous versions, Muscle v5 is much more accurate, is often
faster, and scales to much larger datasets. At the time of writing (late
2021), Muscle v5 has the highest scores on multiple alignment benchmarks
including Balibase, Bralibase, Prefab and Balifam. It can align tens of
thousands of sequences with high accuracy on a low-cost commodity computer
(say, an 8-core Intel CPU with 32 Gb RAM). On large datasets, Muscle v5
is 20-30% more accurate than MAFFT and Clustal-Omega.
Alignment ensembles
Muscle v5 can generate ensembles of high-accuracy alternative alignments.
All replicates have equal average accuracy on benchmark test, including
the MSA made with default parameters. By comparing results of downstream
analysis (trees, structure prediction...) on different replicates, you can
assess the effects of alignment errors on your study.
Topics: Sequence analysis
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muscle3
multiple alignment program of protein sequences
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Versions of package muscle3 |
Release | Version | Architectures |
sid | 3.8.1551-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.8.1551-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.8.1551-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
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License: DFSG free
|
MUSCLE is a multiple alignment program for protein sequences. MUSCLE
stands for multiple sequence comparison by log-expectation. In the
authors tests, MUSCLE achieved the highest scores of all tested
programs on several alignment accuracy benchmarks, and is also one of
the fastest programs out there.
This is version 3 of the muscle program. It is a different program
than muscle version 5 which is packaged as muscle in Debian.
Topics: Sequence analysis
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mustang
multiple structural alignment of proteins
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Versions of package mustang |
Release | Version | Architectures |
trixie | 3.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.2.2-1 | amd64,armel,armhf,i386 |
bullseye | 3.2.3-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 3.2.3-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.2.3-3 | amd64,arm64,armhf,i386 |
sid | 3.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.2.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package mustang: |
biology | peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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Mustang is an algorithm to align multiple protein structures.
Given a set of PDB files, the program uses the spatial
information in the Calpha atoms of the set to produce a sequence alignment.
Based on a progressive pairwise heuristic the algorithm then proceeds
through a number of refinement passes. Mustang reports the multiple
sequence alignment and the corresponding superposition of structures.
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njplot
phylogenetic tree drawing program
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Versions of package njplot |
Release | Version | Architectures |
trixie | 2.4-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.4-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.4-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 2.4-8 | amd64,arm64,armhf,i386 |
jessie | 2.4-2 | amd64,armel,armhf,i386 |
stretch | 2.4-7 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 2.4-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package njplot: |
field | biology, biology:bioinformatics |
interface | x11 |
role | program |
scope | utility |
uitoolkit | motif |
use | analysing, editing, organizing, printing, viewing |
works-with | biological-sequence |
works-with-format | plaintext |
x11 | application |
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License: DFSG free
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NJplot is able to draw any dendrogram expressed in the Newick standard
phylogenetic tree format (e.g., the format used by the Phylip package).
NJplot is especially convenient for rooting the unrooted trees
obtained from parsimony, distance or maximum likelihood tree-building
methods.
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phylip
package of programs for inferring phylogenies
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Versions of package phylip |
Release | Version | Architectures |
bookworm | 3.697+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 3.697+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 3.697+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 3.696+dfsg-1 | amd64,armel,armhf,i386 |
stretch | 3.696+dfsg-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 3.697+dfsg-1 | amd64,arm64,armhf,i386 |
bullseye | 3.697+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package phylip: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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The PHYLogeny Inference Package is a package of programs for inferring
phylogenies (evolutionary trees) from sequences.
Methods that are available in the package include parsimony, distance
matrix, and likelihood methods, including bootstrapping and consensus
trees. Data types that can be handled include molecular sequences, gene
frequencies, restriction sites, distance matrices, and 0/1 discrete
characters.
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phyml
Phylogenetic estimation using Maximum Likelihood
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Versions of package phyml |
Release | Version | Architectures |
stretch | 3.2.0+dfsg-7 | amd64,arm64,armhf,i386 |
sid | 3.3.20220408-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 3.3.20220408-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 3.3.20220408-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 3.3.20200621-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 3.3.20180621-2 | amd64,arm64,armhf,i386 |
jessie | 20120412-2 | amd64,armel,armhf,i386 |
Debtags of package phyml: |
biology | peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
use | analysing, comparing |
works-with | biological-sequence |
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License: DFSG free
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PhyML is a software that estimates maximum likelihood phylogenies from
alignments of nucleotide or amino acid sequences. It provides a wide
range of options that were designed to facilitate standard phylogenetic
analyses. The main strengths of PhyML lies in the large number of
substitution models coupled to various options to search the space of
phylogenetic tree topologies, going from very fast and efficient methods
to slower but generally more accurate approaches. It also implements
two methods to evaluate branch supports in a sound statistical framework
(the non-parametric bootstrap and the approximate likelihood ratio test).
PhyML was designed to process moderate to large data sets. In theory,
alignments with up to 4,000 sequences 2,000,000 character-long can
be analyzed. In practice however, the amount of memory required to process
a data set is proportional of the product of the number of sequences by their
length. Hence, a large number of sequences can only be processed provided
that they are short. Also, PhyML can handle long sequences provided that
they are not numerous. With most standard personal computers, the “comfort
zone” for PhyML generally lies around 3 to 500 sequences less than 2,000
character long.
This package also includes PhyTime.
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poa
Partial Order Alignment for multiple sequence alignment
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Versions of package poa |
Release | Version | Architectures |
buster | 2.0+20060928-7 | amd64,arm64,armhf,i386 |
stretch | 2.0+20060928-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.0+20060928-3 | amd64,armel,armhf,i386 |
bullseye | 2.0+20060928-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 2.0+20060928-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.0+20060928-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 2.0+20060928-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package poa: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
works-with-format | plaintext |
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License: DFSG free
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POA is Partial Order Alignment, a fast program for multiple sequence
alignment (MSA) in bioinformatics. Its advantages are speed,
scalability, sensitivity, and the superior ability to handle branching
/ indels in the alignment. Partial order alignment is an approach to
MSA, which can be combined with existing methods such as progressive
alignment. POA optimally aligns a pair of MSAs and which therefore can
be applied directly to progressive alignment methods such as CLUSTAL.
For large alignments, Progressive POA is 10-30 times faster than
CLUSTALW.
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populations
population genetic software
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Versions of package populations |
Release | Version | Architectures |
stretch | 1.2.33+svn0120106-2.1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.2.33+svn0120106+dfsg-2 | amd64,arm64,armhf,i386 |
jessie | 1.2.33+svn0120106-2.1 | amd64,armel,armhf,i386 |
sid | 1.2.33+svn0120106+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.2.33+svn0120106+dfsg-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.2.33+svn0120106+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.2.33+svn0120106+dfsg-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package populations: |
role | program |
uitoolkit | qt |
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License: DFSG free
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Populations is a population genetic software. It computes genetic
distances between populations or individuals. It builds phylogenetic
trees (NJ or UPGMA) with bootstrap values.
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pplacer
phylogenetic placement and downstream analysis
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Versions of package pplacer |
Release | Version | Architectures |
sid | 1.1~alpha19-8 | amd64,arm64,ppc64el,riscv64,s390x |
bullseye | 1.1~alpha19-4 | amd64,arm64,ppc64el,s390x |
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License: DFSG free
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Pplacer places reads on a phylogenetic tree. guppy (Grand Unified
Phylogenetic Placement Yanalyzer) yanalyzes them. rppr is a helpful tool
for working with reference packages.
Pplacer places query sequences on a fixed reference phylogenetic tree to
maximize phylogenetic likelihood or posterior probability according to a
reference alignment. Pplacer is designed to be fast, to give useful
information about uncertainty, and to offer advanced visualization and
downstream analysis.
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proalign
Probabilistic multiple alignment program
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Versions of package proalign |
Release | Version | Architectures |
stretch | 0.603-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
sid | 0.603-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.603-5 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.603-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.603-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.603-4 | amd64,arm64,armhf,i386 |
jessie | 0.603-1 | amd64,armel,armhf,i386 |
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License: DFSG free
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ProAlign performs probabilistic sequence alignments using hidden Markov
models (HMM). It includes a graphical interface (GUI) allowing to (i)
perform alignments of nucleotide or amino-acid sequences, (ii) view the
quality of solutions, (iii) filter the unreliable alignment regions and
(iv) export alignments to other software.
ProAlign uses a progressive method, such that multiple alignment is
created stepwise by performing pairwise alignments in the nodes of a
guide tree. Sequences are described with vectors of character
probabilities, and each pairwise alignment reconstructs the ancestral
(parent) sequence by computing the probabilities of different
characters according to an evolutionary model.
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probalign
multiple sequence alignment using partition function posterior probabilities
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Versions of package probalign |
Release | Version | Architectures |
bookworm | 1.4-10 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.4-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.4-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.4-8 | amd64,arm64,armhf,i386 |
jessie | 1.4-3 | amd64,armel,armhf,i386 |
sid | 1.4-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.4-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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Probalign uses partition function posterior probability estimates to
compute maximum expected accuracy multiple sequence alignments. It
performs statistically significantly better than the leading alignment
programs Probcons v1.1, MAFFT v5.851, and MUSCLE v3.6 on BAliBASE 3.0,
HOMSTRAD, and OXBENCH benchmarks. Probalign improvements are largest on
datasets containing N/C terminal extensions and on datasets with long
and heterogeneous length sequences. On heteregeneous length datasets
containing repeats Probalign alignment accuracy is 10% and 15% higher
than the other three methods when standard deviation of length is at
least 300 and 400.
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probcons
PROBabilistic CONSistency-based multiple sequence alignment
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Versions of package probcons |
Release | Version | Architectures |
jessie | 1.12-9 | amd64,armel,armhf,i386 |
stretch | 1.12-11 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.12-12 | amd64,arm64,armhf,i386 |
sid | 1.12-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 1.12-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.12-14 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.12-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package probcons: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | comparing |
works-with-format | plaintext |
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License: DFSG free
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Tool for generating multiple alignments of protein sequences. Using a
combination of probabilistic modeling and consistency-based alignment
techniques, PROBCONS has achieved the highest accuracies of all alignment
methods to date. On the BAliBASE benchmark alignment database, alignments
produced by PROBCONS show statistically significant improvement over current
programs, containing an average of 7% more correctly aligned columns than
those of T-Coffee, 11% more correctly aligned columns than those of CLUSTAL W,
and 14% more correctly aligned columns than those of DIALIGN.
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proda
Proteiinisarjojen moninainen rivitys
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Versions of package proda |
Release | Version | Architectures |
bookworm | 1.0-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 1.0-13 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.0-12 | amd64,arm64,armhf,i386 |
stretch | 1.0-10 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.0-8 | amd64,armel,armhf,i386 |
sid | 1.0-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.0-14 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package proda: |
biology | nuceleic-acids, peptidic |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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ProDA on järjestelmä mielivaltaisten proteiinikokoelmien homologisten
alueiden sijoittumisen tunnistamiseen.
Kun syötetään sarja sekvenssejä, ProDA tunnistaa kaikki
yhdessä tai useammassa sekvenssissä esiintyvät homologiset alueet ja
tulostaa näiden alueiden sijaintitiedot.
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prottest
selection of best-fit models of protein evolution
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Versions of package prottest |
Release | Version | Architectures |
trixie | 3.4.2+dfsg-8 | all |
sid | 3.4.2+dfsg-8 | all |
stretch | 3.4.2+dfsg-2 | all |
bookworm | 3.4.2+dfsg-8 | all |
bullseye | 3.4.2+dfsg-5 | all |
buster | 3.4.2+dfsg-3 | all |
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License: DFSG free
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PROTTEST (ModelTest's relative) is a program for selecting the model of
protein evolution that best fits a given set of sequences (alignment).
This java program is based on the Phyml program (for maximum likelihood
calculations and optimization of parameters) and uses the PAL library as
well. Models included are empirical substitution matrices (such as WAG,
LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam,
MtArt, HIVb, and HIVw) that indicate relative rates of amino acid
replacement, and specific improvements (+I:invariable sites, +G: rate
heterogeneity among sites, +F: observed amino acid frequencies) to
account for the evolutionary constraints impossed by conservation of
protein structure and function. ProtTest uses the Akaike Information
Criterion (AIC) and other statistics (AICc and BIC) to find which of the
candidate models best fits the data at hand.
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quicktree
Neighbor-Joining algorithm for phylogenies
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Versions of package quicktree |
Release | Version | Architectures |
bookworm | 2.5-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 2.5-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 2.5-5 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 2.5-6 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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QuickTree is an efficient implementation of the Neighbor-Joining
algorithm (PMID: 3447015), capable of reconstructing phylogenies from
huge alignments in time less than the age of the universe.
QuickTree accepts both distance matrix and multiple-sequence-aligment
inputs. The former should be in PHYLIP format. The latter should be
in Stockholm format, which is the native alignment format for the Pfam
database. Alignments in various formats can be converted to Stockholm
format with the sreformat program, which is part of the HMMer package
(hmmer.org).
The tress are written to stdout, in the Newick/New-Hampshire format
use by PHYLIP and many other programs
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seaview
Multiplatform interface for sequence alignment and phylogeny
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Versions of package seaview |
Release | Version | Architectures |
buster | 4.7-1 | amd64,arm64,armhf,i386 |
stretch | 4.6.1.2-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 4.5.3.1-2 | amd64,armel,armhf,i386 |
bookworm | 5.0.5-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 5.0.5-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 5.0.5-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 5.0.4-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
Debtags of package seaview: |
field | biology, biology:bioinformatics |
interface | x11 |
network | client |
role | program |
scope | utility |
uitoolkit | fltk |
use | comparing, editing, printing, viewing |
works-with | biological-sequence |
works-with-format | plaintext |
x11 | application |
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License: DFSG free
|
SeaView is a viewer and editor of multiple sequence alignments, i.e.
DNA or protein sequences are positioned each in their own separate line,
such that the nucleotide/amino acid at a particular position (column) is
presumed to have the same biochemical property.
SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA,
PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees.
Alignments can be manually edited. It drives the programs Muscle or Clustal
Omega for multiple sequence alignment, and also allows one to use any external
alignment algorithm able to read and write FASTA-formatted files. It computes
phylogenetic trees by parsimony using PHYLIP's dnapars/protpars algorithm, by
distance with NJ or BioNJ algorithms on a variety of evolutionary distances, or
by maximum likelihood using the program PhyML 3.0.
SeaView draws phylogenetic
trees on screen or PostScript files, and allows one to download sequences from
EMBL/GenBank/UniProt using the Internet.
The package is enhanced by the following packages:
muscle
muscle3
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sigma-align
Simple greedy multiple alignment of non-coding DNA sequences
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Versions of package sigma-align |
Release | Version | Architectures |
sid | 1.1.3-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
stretch | 1.1.3-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 1.1.3-6 | amd64,arm64,armhf,i386 |
bullseye | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 1.1.3-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 1.1.3-9 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 1.1.3-3 | amd64,armel,armhf,i386 |
Debtags of package sigma-align: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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Sigma (“Simple greedy multiple alignment”) is an alignment program. It's
algorithm and scoring scheme are designed specifically for non-coding
DNA sequence.
It uses a strategy of seeking the best possible gapless local
alignments. This happens at each step making the best possible alignment
consistent with existing alignments. It scores the significance of the
alignment based on the lengths of the aligned fragments and a background
model. These may be supplied or estimated from an auxiliary file of
intergenic DNA.
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spread-phy
analyze and visualize phylogeographic reconstructions
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Versions of package spread-phy |
Release | Version | Architectures |
stretch | 1.0.7+dfsg-1 | all |
jessie | 1.0.5+dfsg-1 (contrib) | all |
buster | 1.0.7+dfsg-2 | all |
bullseye | 1.0.7+dfsg-3 | all |
bookworm | 1.0.7+dfsg-5 | all |
trixie | 1.0.7+dfsg-5 | all |
sid | 1.0.7+dfsg-5 | all |
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License: DFSG free
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SPREAD is a user-friendly application to analyze and visualize
phylogeographic reconstructions resulting from Bayesian inference of
spatio-temporal diffusion.
There is a tutorial for SPREAD online at
http://www.kuleuven.be/aidslab/phylogeography/tutorial/spread_tutorial.html
Originally this program is named "spread". However, there is just such a
package inside Debian and thus a 'phy' for phylogeny was prepended.
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t-coffee
Multiple Sequence Alignment
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Versions of package t-coffee |
Release | Version | Architectures |
jessie | 11.00.8cbe486-1 | amd64,armel,armhf,i386 |
sid | 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 13.45.0.4846264+really13.41.0.28bdc39+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 13.41.0.28bdc39+dfsg-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 12.00.7fb08c2-4 | amd64,arm64,armhf,i386 |
stretch | 11.00.8cbe486-5 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
Debtags of package t-coffee: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
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.
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tm-align
structural alignment of proteins
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Versions of package tm-align |
Release | Version | Architectures |
sid | 20190822+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 20140601+dfsg-1 | amd64,armel,armhf,i386 |
stretch | 20160521+dfsg-2 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 20170708+dfsg-2 | amd64,arm64,armhf,i386 |
bullseye | 20190822+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 20190822+dfsg-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 20190822+dfsg-3 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
Debtags of package tm-align: |
role | program |
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License: DFSG free
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TM-align is a computer algorithm for protein structure alignment using
dynamic programming. The scoring is performed by the TM-score rotation
matrix. This is similar to the RMSD in that unaligned portions of the
structure influence the scoring less than the more structurally conserved
regions.
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tree-ppuzzle
Parallelized reconstruction of phylogenetic trees by maximum likelihood
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Versions of package tree-ppuzzle |
Release | Version | Architectures |
bullseye | 5.3~rc16+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bookworm | 5.3~rc16+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
trixie | 5.3~rc16+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
sid | 5.3~rc16+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 5.2-7 | amd64,armel,armhf,i386 |
stretch | 5.2-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
buster | 5.2-11 | amd64,arm64,armhf,i386 |
Debtags of package tree-ppuzzle: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
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License: DFSG free
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TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that
implements a fast tree search algorithm, quartet puzzling, that allows
analysis of large data sets and automatically assigns estimations of support
to each internal branch. TREE-PUZZLE also computes pairwise maximum
likelihood distances as well as branch lengths for user specified trees.
Branch lengths can also be calculated under the clock-assumption. In
addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment.
This is the parallelized version of tree-puzzle.
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tree-puzzle
Reconstruction of phylogenetic trees by maximum likelihood
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Versions of package tree-puzzle |
Release | Version | Architectures |
sid | 5.3~rc16+dfsg-11 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bullseye | 5.3~rc16+dfsg-8 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
jessie | 5.2-7 | amd64,armel,armhf,i386 |
bookworm | 5.3~rc16+dfsg-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 5.2-8 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
trixie | 5.3~rc16+dfsg-10 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
buster | 5.2-11 | amd64,arm64,armhf,i386 |
Debtags of package tree-puzzle: |
field | biology, biology:bioinformatics |
interface | commandline |
role | program |
scope | utility |
use | analysing, comparing |
works-with-format | plaintext |
|
License: DFSG free
|
TREE-PUZZLE (the new name for PUZZLE) is an interactive console program that
implements a fast tree search algorithm, quartet puzzling, that allows
analysis of large data sets and automatically assigns estimations of support
to each internal branch. TREE-PUZZLE also computes pairwise maximum
likelihood distances as well as branch lengths for user specified trees.
Branch lengths can also be calculated under the clock-assumption. In
addition, TREE-PUZZLE offers a novel method, likelihood mapping, to
investigate the support of a hypothesized internal branch without
computing an overall tree and to visualize the phylogenetic content of
a sequence alignment.
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treeview
Java re-implementation of Michael Eisen's TreeView
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Versions of package treeview |
Release | Version | Architectures |
jessie | 1.1.6.4+dfsg-1 (contrib) | all |
sid | 1.2.0+dfsg-2 | all |
trixie | 1.2.0+dfsg-2 | all |
stretch | 1.1.6.4+dfsg1-2 | all |
buster | 1.1.6.4+dfsg1-4 | all |
bullseye | 1.2.0+dfsg-1 | all |
bookworm | 1.2.0+dfsg-1 | all |
upstream | 1.2.1 |
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License: DFSG free
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TreeView creates a matrix-like display of expression data, known as
Eisen clustering. The original implementation was a Windows program
named TreeView by Michael Eisen. This TreeView package, sometimes also
referred to as jTreeView, was rewritten in Java under a free license.
Java TreeView is an extensible viewer for microarray data in
PCL or CDT format.
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treeviewx
Displays and prints phylogenetic trees
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Versions of package treeviewx |
Release | Version | Architectures |
stretch | 0.5.1+20100823-4 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 0.5.1+20100823-3 | amd64,armel,armhf,i386 |
sid | 0.5.1+git20100823.7e4d0e9-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 0.5.1+git20100823.7e4d0e9-4 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 0.5.1+git20100823.7e4d0e9-4 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 0.5.1+git20100823.7e4d0e9-3 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 0.5.1+git20100823.7e4d0e9-1 | amd64,arm64,armhf,i386 |
Debtags of package treeviewx: |
field | biology, biology:bioinformatics |
interface | x11 |
role | program |
scope | utility |
uitoolkit | wxwidgets |
use | viewing |
works-with-format | pdf, plaintext, postscript, svg |
x11 | application |
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License: DFSG free
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TreeView X is an open source and multi-platform program to display
phylogenetic trees. It can read and display NEXUS and Newick format tree files
(such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It
allows one to order the branches of the trees, and to export the trees in SVG
format.
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veryfasttree
Speeding up the estimation of phylogenetic trees from sequences
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Versions of package veryfasttree |
Release | Version | Architectures |
sid | 4.0.4+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 4.0.3+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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VeryFastTree is a highly efficient implementation inspired by the FastTree-2
tool, designed to expedite the inference of approximately-maximum-likelihood
phylogenetic trees from nucleotide or protein sequence alignments. It is an
optimized implementation designed to accelerate the estimation of phylogenies
for large alignments. By leveraging parallelization and vectorization
strategies, VeryFastTree significantly improves the performance and
scalability of phylogenetic analysis, allowing it to construct phylogenetic
trees in a fraction of the time previously required.
Maintaining the integrity of FastTree-2, VeryFastTree retains the same phases,
methods, and heuristics used for estimating phylogenetic trees. This ensures
that the topological accuracy of the trees produced by VeryFastTree remains
equivalent to that of FastTree-2. Moreover, unlike the parallel version of
FastTree-2, VeryFastTree guarantees deterministic results, eliminating any
potential variations in the output.
To facilitate a seamless transition for users, VeryFastTree adopts the exact
same command line arguments as FastTree-2. This means that by simply
substituting FastTree-2 with VeryFastTree, and using the same set of options,
users can significantly enhance the overall performance of their phylogenetic
analyses.
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Official Debian packages with lower relevance
python3-treetime
inference of time stamped phylogenies and ancestral reconstruction (Python 3)
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Versions of package python3-treetime |
Release | Version | Architectures |
sid | 0.11.1-1 | all |
buster | 0.5.3-1 | all |
bullseye | 0.8.1-1 | all |
bookworm | 0.9.4-1 | all |
trixie | 0.11.1-1 | all |
upstream | 0.11.4 |
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License: DFSG free
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TreeTime provides routines for ancestral sequence reconstruction and the
maximum likelihoo inference of molecular-clock phylogenies, i.e., a tree
where all branches are scaled such that the locations of terminal nodes
correspond to their sampling times and internal nodes are placed at the
most likely time of divergence.
TreeTime aims at striking a compromise between sophisticated
probabilistic models of evolution and fast heuristics. It implements GTR
models of ancestral inference and branch length optimization, but takes
the tree topology as given. To optimize the likelihood of time-scaled
phylogenies, treetime uses an iterative approach that first infers
ancestral sequences given the branch length of the tree, then optimizes
the positions of unconstraine d nodes on the time axis, and then repeats
this cycle. The only topology optimization are (optional) resolution of
polytomies in a way that is most (approximately) consistent with the
sampling time constraints on the tree. The package is designed to be
used as a stand-alone tool or as a library used in larger phylogenetic
analysis workflows.
Features
- ancestral sequence reconstruction (marginal and joint maximum
likelihood)
- molecular clock tree inference (marginal and joint maximum
likelihood)
- inference of GTR models
- rerooting to obtain best root-to-tip regression
- auto-correlated relaxed molecular clock (with normal prior)
This package provides the Python 3 module.
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Packaging has started and developers might try the packaging code in VCS
forester
Graphical vizualiation tool Archaeopteryx
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Versions of package forester |
Release | Version | Architectures |
VCS | 0.0+20180205-1 | all |
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License: LGPL 2.1+
Debian package not available
Version: 0.0+20180205-1
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Archaeopteryx is a software tool for the visualization, analysis,
and editing of potentially large and highly annotated phylogenetic trees.
It can be used both as applet (ArchaeopteryxA and ArchaeopteryxE) and
as a standalone application.
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patristic
Calculate patristic distances and comparing the components of genetic change
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Versions of package patristic |
Release | Version | Architectures |
VCS | 0.0.20100817-2 | all |
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License: free
Debian package not available
Version: 0.0.20100817-2
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Patristic overcomes some logistic barriers to analysing signals in
sequences. In additional to calculating patristic distances, it provides
plots for any combination of matrices, calculates commonly used
statistics, allows data such as isolation dates to be entered and
reorders matrices with matching species or gene labels. It will be used
to analyse rates of mutation and substitutional saturation and the
evolution of viruses.
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No known packages available but some record of interest (WNPP bug)
Graphical interface for molecular phylogenetic inference
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License: unknown
Debian package not available
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Phylo_win is a graphical colour interface for molecular phylogenetic
inference. It performs neighbor-joining, parsimony and maximum
likelihood methods and bootstrap with any of them. Many distances can be
used including Jukes & Cantor, Kimura, Tajima & Nei, HKY, Galtier & Gouy
(1995), LogDet for nucleotidic sequences, Poisson correction for protein
sequences, Ka and Ks for codon sequences. Species and sites to include
in the analysis are selected by mouse. Reconstructed trees can be drawn,
edited, printed, stored and evaluated according to numerous criteria.
This program uses sources files from the Phylip program, which forbids
its use for profit. Therfore, Phylo_win will unfortunately have to be
distributed in contrib or non-free.
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No known packages available
gbioseq
DNA sequence editor for Linux
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License: GPL
Debian package not available
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gBioSeq is in an early stage of development, but it is already running.
The goal is to provide an easy to use software to edit DNA sequences under
Linux, Windows, MacOsX, using GTK C# (Mono).
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jstreeview
Editor for Phylogenetic Trees
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License: MIT/X11
Debian package not available
Language: JavaScript
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A concise viewer/editor for phylogenetic trees in the Newick format.
The core functions are written in JavaScript, using the canvas tag
proposed by HTML 5. No server side support is needed for rendering the
picture and therefore you can grab this page together with knhx.js and
canvastext.js to locally view your trees in a supported web browser.
The source can be downloaded at
http://www.sanger.ac.uk/Users/lh3/download/jstreeview.zip
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phpphylotree
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License: GPL
Debian package not available
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PhpPhylotree is a web application that is able to draw phylogenetic trees.
It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.
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treetime
Bayesian sampling of phylogenetic trees from molecular data
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License: GPL
Debian package not available
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TreeTime is controlled by input files in nexus format and does
bayesian sampling of phylogenetic trees from these data.
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