Package: bioperl-run (1.7.3-9)

[ Source: bioperl-run  ]

BioPerl wrappers: scripts

Contains scripts from the BioPerl-Run package. This package will also install all wrappable applications packaged in Debian. The ones that are not Free are "Suggested" by this package.

Tags: Field: Biology, Bioinformatics, Implemented in: implemented-in::perl, interface::commandline, Role: Program

Other Packages Related to bioperl-run

• dep: bioperl (>= 1.7.4)

  Perl tools for computational molecular biology

• dep: default-jdk-headless

  Standard Java or Java compatible Development Kit (headless)

• dep: hyphy-pt

  Hypothesis testing using Phylogenies (pthreads version)

  or hyphy-mpi

  Hypothesis testing using Phylogenies (MPI version)

• dep: libbio-cluster-perl

  BioPerl cluster modules

• dep: libbio-eutilities-perl

  BioPerl interface to the Entrez Programming Utilities (E-utilities)

• dep: libbio-featureio-perl

  Modules for reading, writing, and manipulating sequence features

• dep: libbio-perl-run-perl (= 1.7.3-9)

  BioPerl wrappers: modules

• dep: libbio-tools-run-alignment-clustalw-perl

  Bioperl interface to Clustal W

• 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: libtest-requiresinternet-perl

  module to easily test network connectivity

• dep: perl

  Larry Wall's Practical Extraction and Report Language

• rec: amap-align

  Protein multiple alignment by sequence annealing

• rec: bedtools

  suite of utilities for comparing genomic features

• rec: bowtie

  Ultrafast memory-efficient short read aligner

• rec: bwa

  Burrows-Wheeler Aligner

• rec: clustalw

  global multiple nucleotide or peptide sequence alignment

• rec: emboss

  European molecular biology open software suite

• rec: exonerate

  generic tool for pairwise sequence comparison

• rec: hmmer

  profile hidden Markov models for protein sequence analysis

• rec: infernal

  inference of RNA secondary structural alignments

• rec: kalign

  Global and progressive multiple sequence alignment

• rec: lagan

  highly parametrizable pairwise global genome sequence aligner

• rec: mafft

  Multiple alignment program for amino acid or nucleotide sequences

• rec: maq

  maps short fixed-length polymorphic DNA sequence reads to reference sequences

• rec: muscle

  Multiple alignment program of protein sequences

• rec: ncbi-blast+-legacy

  NCBI Blast legacy call script

• rec: ncoils

  coiled coil secondary structure prediction

• rec: pal2nal

  converts proteins to genomic DNA alignment

• rec: pftools

  build and search protein and DNA generalized profiles

• rec: phylip

  package of programs for inferring phylogenies

• rec: phyml

  Phylogenetic estimation using Maximum Likelihood

• 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: samtools

  processing sequence alignments in SAM, BAM and CRAM formats

• rec: sim4

  tool for aligning cDNA and genomic DNA

• rec: t-coffee

  Multiple Sequence Alignment

• rec: tigr-glimmer

  Gene detection in archea and bacteria

• rec: wise

  comparison of biopolymers, like DNA and protein sequences

• sug: fasta3

  tools for searching collections of biological sequences

• sug: gmap

  spliced and SNP-tolerant alignment for mRNA and short reads

• sug: trnascan-se

  detection of transfer RNA genes in genomic sequence

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