ARIADNE is a package of two programs, ariadne and prospero, that compare
protein sequences and profiles using the Smith-Waterman algorithm, and
assesses statistical significance using a new accurate formula,
described in Mott, 2000, "Accurate Formula for P-values of gapped local
sequence and profile alignments" J. Mol Biol. 300:649-659.
The sequence/profile comparison algorithms used in ARIADNE are standard,
and are probably not the fastest implementations available. The novel
part is the method for determining statistical significance, which will
give thresholds of significance that are accurate to within 5% 95% of
the time.
The package is written in ANSI C. You are free to incorporate the method
used for assessing statistical significance into third-party code,
provided you cite the above reference. The routines for assessing
significance are all in gaplib.c
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.
BWA is a program for aligning sequencing reads against a large reference
genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.
CD-HIT is a very widely used program for clustering and comparing protein or
nucleotide sequences.
Consed is a tool for viewing and editing sequence assemblies made by phrap,
and includes Autofinish which will automatically choose finishing reads.
The FASTX-Toolkit is a collection of command line tools for Short-Reads
FASTA/FASTQ files preprocessing.
LAMARC (Likelihood Analysis with Metropolis Algorithm using Random
Coalescence) is a package of programs for computing population parameters
such as population size, population growth rate and migration rates. It does
this by using likelihoods for samples of data (sequences, microsatellites,
and electrophoretic polymorphisms) from populations.
Visualizing the results of molecular orbital calculations
1) MO program: gaussian, gamess, mopac, etc.
2) display molecule in 3D: geo-opt, single-point, nomal mode (animation)
3) density: contour plot or 3D view for electron density and MO coefficient
Everything what you want about MO calculation can be seen.
By the distribution policy of the author;
* Only the latest version is supplied.
* Users must get the `distfiles' from the original site.
* Do not re-distribute the source and the executable.
* Using a not-so-latest version is prohibited, because
the author may only respond about the latest version.
A standalone program for mapping and aligning cDNA sequences to a
genome. The program maps and aligns a single sequence with minimal
startup time and memory requirements, and provides fast batch
processing of large sequence sets. The program generates accurate
gene structures, even in the presence of substantial polymorphisms
and sequence errors, without using probabilistic splice site models.
Methodology underlying the program includes a minimal sampling
strategy for genomic mapping, oligomer chaining for approximate
alignment, sandwich DP for splice site detection, and microexon
identification with statistical significance testing.
Gperiodic displays a periodic table of the elements, allowing you to
browse through the elements, and view detailed information about each
element.