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The Linux for Biotechnology project (LfB)致力于收集各种Linux系统环境下的生物技术相关软件,并提供方便的点击安装操作及相关文献等等。原始网站。
LFB计划的实施,使得生物学家可以用普通的PC机便可完成非常昂贵的服务器才能完成的工作。目前的LFB包括以下linux系统下的生物软件,资料加文献共计480M,解压后超过1G的内容,均加入到赠品光盘11,zp11中:
- abacus - Analysis
of Blake's Conjecture Using Simulations
- ae2 - Sequence alignment editor
- alfresco -
Comparitive sequence analysis
-
artemis - DNA sequence viewer and annotation tool
- beta - Estimation
of alpha - Nonparametric linkage analysis
- biomail
- web-based application for medical researchers and biologists.
- bioperl - perl tools
for Molecular biology
- biopython -
Python tools for Molecular biology
- codonW- A package
for codon usage analysis.
- DEODAS
- DEgenerate Oligonucleotide Design & Analysis System
- Distutils - Python distribution tools
- DND - Protein molecular dynamics simulation/visualization
-
DomainFinder - An interactive program for the determination and
characterization of dynamical domains in proteins.
- dx - Data Explorer,
visualisation package
- e-PCR - Sequence
mapping by Electronic PRC
- EdIt
- An automatic editor for DNA sequence data
- efetch - Retrieve
entries from sequence databases
-
EMBOSS - EMB Open Source Software
- ESPript - Creates
postrcipt sequence renderings
- fastlink
- Genetic linkage computations
- garlic
- Molecular visualization
- GenoCheck -
A method for detecting errors in pedigree data
- genpak
- Utilities to manipulate DNA sequences
- gmaes - Evolution
simulations
- gperiodic -
Periodic table
- gibbs -
Calculation of Probabilities for Diallelic Traits on Complex Pedigrees
- hmmer - Biological
sequence analysis using profile hidden Markov models
- ImageJ - Java
Image viewer
- jalview
- a java multiple alignment editor
- jmol
- an open-source molecule viewer and editor
- kmol
- Molecular weight calculator
- ldb_2b - Hybrid mapping
- LEKSBOT - a botanical lexicon
- lintre - Phylogenetic
tests of the molecular clock and linearized tree
- melting
- nearest-neighbor computation of nucleic acid hybridation
- MIRA
- DNA shotgun sequence data assembler
-
mmlib - A C++ macromolecular class library
-
mmtool - A macromolecular visualisation tool
- pdbtool
- A macromolecular visualisation tool
- moldy -
a general-purpose molecular dynamics simulation program
- ncbi-tools -
NCBI Software Development Toolkit was developed for the production and
distribution of GenBank, Entrez, BLAST, and related services by NCBI.
- Blastall
- NHGRI Blastall (a perl interface)
- njbafd -
Neighbor-joining tree construction from allele frequency data
- njbtie - search
all tie neighbor-joining trees and UPGMA trees and for bootstrapping
- oligomap - OLIGOMAP
is a tool to help researchers engineer restriction sites into oligonucleotides
by silent mutagenesis
- orfind -
orfind is a command line version of ORF Finder (http://www.ncbi.nlm.nih.gov/gorf/gorf.html)
- pdb2cif
- convert PDB to CIF format
- pftools - pftools
is a collection of experimental programs supporting the generalized
profile format and search method of PROSITE and NUCSITE.
- pima - Pattern-Induced
Multi-sequence Alignment program
- pseudoknots
- An extension of the Zuker M FOLD algorithm to optimal minimum energy
prediction of pseudoknotted RNA structures
- plato - Partial
likelihoods expressed through optimisation
- primer3
- Primer3 picks primers for PCR reactions
- PSPP - Statistical
analysis package.
- puzzle
- Maximum likelihood analysis for nucleotide, amino acid, and two-state
data
- PSeq-Gen -
An application for the Monte Carlo simulation of protein sequence evolution
along phylogenetic trees
- QDate - Estimates
date of divergence using data for sequence parirs
- QuickPDB - Java Applet
to view Protein Data Bank
- rhmapper
- A package for creating radiation hybrid maps
- rnabob - searches
for RNA motifs in sequence databases
-
SampLin - Data Acquisition package
- sc_rate - Evaluates the quality of any sequence alignment.
- Topal - Package for Detecting Recombination Breakpoints
- RasMol2 - molecular
graphics program intended for the visualisation of proteins, nucleic
acids and small molecules.
- pasu - Probability and Statistics Utilities
- PVM - Parallel
Virtual Machine
- PyMOL - molecular
graphics program designed for rapid and efficient generation of high-quality
molecular graphics animations.
-
seals - System for Easy Analysis of Lots of Sequences
- sendbs - Average
nucleotide diversity within and between populations
- sequin
- Program to aid submission of sequences to GenBank, EMBL and DDJB
- seqsplit - Programs
for running blastx on very long queries
- sibs - Sib Pair
Analysis
- simPCR - check
an sfind file from GCG for sequences that have homology to 2 opposite
primers.
- sog - algorithm
to find the most parsimoneous nucleotide phylogenetic tree
- TipDate -
A program to estimate the rate of molecular evolution and time-scale
of a phylogeny from dated sequences.
- tRNAscan
- a program for improved detection of transfer RNA genes in genomic
sequence
- treevolve
- a program to simulate the evolution of DNA sequences under different
population dynamic scenarios
- vanilla
- command line programs (written in Java) to provide simple access to
the functionality of PAL
- vaspview - scientific
visualization package for examining output files generated by the Vienna
Ab-initio Simulation Package
- w2h - WWW interface to the GCG Sequence Analysis Software Package
- wise
- DNA and protein sequence comparison package
所有以上软件均在RedHat (v6.2) 和SuSE
(version 6.4)下测试通过。
以上软件,均加入到赠品光盘11,zp11中:
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