Packages / Debian 13 (Trixie) / science / bioperl-run
Package: bioperl-run (1.7.3-13)
Maintainers:
External Resources:
Homepage: [metacpan.org]
BioPerl wrappers: scripts
Other Packages Related to bioperl-run:
dep: [perl] [any]
Larry Wall's Practical Extraction and Report Language
dep: [bioperl] (>= 1.7.4)
Perl tools for computational molecular biology
dep: [libbio-perl-run-perl] (= 1.7.3-13)
BioPerl wrappers: modules
dep: [libbio-featureio-perl]
Modules for reading, writing, and manipulating sequence features
dep: [libbio-cluster-perl]
BioPerl cluster modules
dep: [libtest-requiresinternet-perl]
module to easily test network connectivity
dep: [libbio-eutilities-perl]
BioPerl interface to the Entrez Programming Utilities (E-utilities)
dep: [libbio-tools-run-remoteblast-perl]
Object for remote execution of the NCBI Blast via HTTP
dep: [libsoap-lite-perl]
Perl implementation of a SOAP client and server
dep: [default-jdk-headless]
Standard Java or Java compatible Development Kit (headless)
rec: [amap-align]
Protein multiple alignment by sequence annealing
rec: [ncbi-blast+-legacy]
NCBI Blast legacy call script
rec: [bwa]
Burrows-Wheeler Aligner
rec: [exonerate]
generic tool for pairwise sequence comparison
rec: [kalign]
Global and progressive multiple sequence alignment
rec: [maq]
maps short fixed-length polymorphic DNA sequence reads to reference sequences
rec: [mafft]
Multiple alignment program for amino acid or nucleotide sequences
rec: [muscle]
Multiple alignment program of protein sequences
rec: [ncoils]
coiled coil secondary structure prediction
rec: [phylip]
package of programs for inferring phylogenies
rec: [primer3]
tool to design flanking oligo nucleotides for DNA amplification
rec: [probalign]
multiple sequence alignment using partition function posterior probabilities
rec: [probcons]
PROBabilistic CONSistency-based multiple sequence alignment
rec: [raxml]
Randomized Axelerated Maximum Likelihood of phylogenetic trees
rec: [sim4]
tool for aligning cDNA and genomic DNA
rec: [t-coffee]
Multiple Sequence Alignment
rec: [wise]
comparison of biopolymers, like DNA and protein sequences
rec: [lagan]
highly parametrizable pairwise global genome sequence aligner
rec: [pal2nal]
converts proteins to genomic DNA alignment
sug: [gmap]
spliced and SNP-tolerant alignment for mRNA and short reads
sug: [fasta3]
tools for searching collections of biological sequences
sug: [trnascan-se]
detection of transfer RNA genes in genomic sequence
sug: [bedtools]
suite of utilities for comparing genomic features
sug: [bowtie]
Ultrafast memory-efficient short read aligner
sug: [clustalw]
global multiple nucleotide or peptide sequence alignment
sug: [emboss]
European molecular biology open software suite
sug: [hmmer]
profile hidden Markov models for protein sequence analysis
sug: [hyphy-pt]
Hypothesis testing using Phylogenies (pthreads version)
sug: [hyphy-mpi]
Hypothesis testing using Phylogenies (MPI version)
sug: [infernal]
inference of RNA secondary structural alignments
sug: [libbio-tools-run-alignment-clustalw-perl]
Bioperl interface to Clustal W
sug: [pftools]
build and search protein and DNA generalized profiles
sug: [phyml]
Phylogenetic estimation using Maximum Likelihood
sug: [samtools]
processing sequence alignments in SAM, BAM and CRAM formats
sug: [tigr-glimmer]
Gene detection in archea and bacteria
Download bioperl-run
| Architecture | Package Size | Installed Size | Files |
|---|---|---|---|
| all | 36 KiB | 89 KiB | [list of files] |
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Field source: Debian 13 (Trixie) main amd64 revision trixie-main-amd64:3ab4e811cf4f3e5a335d382c58cc19d85f1abe7a4ef4689160ca1f637fa0e9b3