Biotechnology resources on the Internet
Linux software index - science
Scientific Applications for Linux -
Chemistry, Biology and related
abacus - Analysis of Blake's Conje
cture Using Simulations
alfresco - Comparitive sequence a
nalysis
artemis - DNA sequ
ence viewer and annotation tool
beta - Estimation of alpha - Non
parametric linkage analysis
biomail - web-based applicatio
n for medical researchers and biologists.
bioperl - perl tools for Molecular biolo
gy
biopython - Python tools for Molec
ular biology
codonW- A package for codon usage a
nalysis.
DEODAS - DEgenerate Oligonucleo
tide Design & Analysis System
DomainFinder - An
interactive program for the determination and characterization of dynamical doma
ins in proteins.
dx - Data Explorer, visualisation pack
age
e-PCR - Sequence mapping by Electron
ic PRC
EdIt - An automatic ed
itor for DNA sequence data
efetch - Retrieve entries from sequen
ce databases
EMBOSS - EMB Open S
ource Software
ESPript - Creates postrcipt sequence rende
rings
fastlink - Genetic linkage comput
ations
garlic - Molecular visualizati
on
GenoCheck - A method for detecting
errors in pedigree data
genpak - Utilit
ies to manipulate DNA sequences
gmaes - Evolution simulations
gperiodic - Periodic table
gibbs - Calculation of Probabili
ties for Diallelic Traits on Complex Pedigrees
hmmer - Biological sequence analysis
using profile hidden Markov models
ImageJ - Java Image viewer
jalview - a java mul
tiple alignment editor
jmol - an open-source molecu
le viewer and editor
kmol - Molecular weight c
alculator
lintre - Phylogenetic tests of the m
olecular clock and linearized tree
melting - ne
arest-neighbor computation of nucleic acid hybridation
MIRA - DNA shotgun seq
uence data assembler
mmlib - A C++ macro
molecular class library
mmtool - A macromol
ecular visualisation tool
pdbtool - A macromol
ecular visualisation tool
moldy - a general-purpose mole
cular dynamics simulation program
ncbi-tools - NCBI Software Developmen
t Toolkit was developed for the production and distribution of GenBank, Entrez,
BLAST, and related services by NCBI.
Blastall - NHGR
I Blastall (a perl interface)
njbafd - Neighbor-joining tree co
nstruction from allele frequency data
njbtie - search all tie neighbor-joinin
g trees and UPGMA trees and for bootstrapping
oligomap - OLIGOMAP is a tool to help r
esearchers engineer restriction sites into oligonucleotides by silent mutagenesi
s
orfind - orfind is a command li
ne version of ORF Finder
pdb2cif - convert PDB
to CIF format
pftools - pftools is a collection o
f experimental programs supporting the generalized profile format and search met
hod of PROSITE and NUCSITE.
pima - Pattern-Induced Multi-sequence Alig
nment program
pseudoknots - An extension of the
Zuker M FOLD algorithm to optimal minimum energy prediction of pseudoknotted RNA
structures
plato - Partial likelihoods expre
ssed through optimisation
pr
imer3 - Primer3 picks primers for PCR reactions
PSPP - Statistical analysis package.
puzzle - Maximum likel
ihood 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 diverge
nce using data for sequence parirs
QuickPDB - Java Applet to view Protein Da
ta Bank
rhmapper - A pa
ckage for creating radiation hybrid maps
rnabob - searches for RNA motifs in
sequence databases
SampLin - Data A
cquisition package
RasMol2 - molecular graphic
s program intended for the visualisation of proteins, nucleic acids and small mo
lecules.
PVM - Parallel Virtual Machine
PyMOL - molecular graphics program desi
gned for rapid and efficient generation of high-quality molecular graphics anima
tions.
seals - System for
Easy Analysis of Lots of Sequences
sendbs - Average nucleotide diversity w
ithin and between populations
sequin - Program to aid s
ubmission 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 f
or sequences that have homology to 2 opposite primers.
sog - algorithm to find the most parsimo
neous nucleotide phylogenetic tree
TipDate - A program to estimate t
he rate of molecular evolution and time-scale of a phylogeny from dated sequence
s.
tRNAscan - a program for improv
ed 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 lin
e programs (written in Java) to provide simple access to the functionality of PA
L
vaspview - scientific visuali
zation 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 sequ
ence comparison package