Pathrate is a tool that can estimate the capacity of network paths. An
important feature of Pathrate is that it is robust to cross traffic
effects, meaning that it can measure the path capacity even when the
path is significantly loaded. This is crucial, since the hardest paths
to measure are the heavily loaded ones.
Pipebench shows the current throughput and amount of data going through a
pipe. It can be used to show the progress of a large md5sum process:
cat bigfile | pipebench | md5sum.
- Michael L. Hostbaek
mich@FreeBSD.org
This is an ANSI C version of the SciMark2 benchmark, translated from the
original Java sources. The intent in making this benchmark available in
C is mainly for performance comparisons.
Results of this benchmark can be sent to pozo@nist.gov.
UnixBench v4.1 based on the BYTE UNIX Benchmarks v3.
Artemis is a DNA sequence viewer and annotation tool that allows
visualisation of sequence features and the results of analyses within
the context of the sequence, and its six-frame translation. Artemis is
written in Java, reads EMBL or GENBANK format sequences and feature
tables, and can work on sequences of any size.
ACT (Artemis Comparison Tool) is a DNA sequence comparison viewer based
on Artemis. It can open two or more sequences (and their
annotations/features) together with their comparisons (usually the
result of running blastn or tblastx searches).
DIAMOND is a BLAST-compatible local aligner for mapping protein and translated
DNA query sequences against a protein reference database (BLASTP and BLASTX
alignment mode). The speedup over BLAST is up to 20,000 on short reads at a
typical sensitivity of 90-99% relative to BLAST depending on the data and
settings.
fastDNAml is a program derived from Joseph Felsenstein's version 3.3 DNAML
(part of his PHYLIP package). Users should consult the documentation for
DNAML before using this program.
fastDNAml is an attempt to solve the same problem as DNAML, but to do so
faster and using less memory, so that larger trees and/or more bootstrap
replicates become tractable. Much of fastDNAml is merely a recoding of the
PHYLIP 3.3 DNAML program from PASCAL to C.
gff2ps is a script program developed with the aim of converting
gff-formatted records into high quality one-dimensional plots in
PostScript. Such plots maybe useful for comparing genomic structures
and to visualizing outputs from genome annotation programs.
Phylogenetic Analysis by Maximum Likelihood (PAML)
PAML is a package of programs for phylogenetic analyses of DNA or protein
sequences using maximum likelihood. It is not good for tree making. It may be
used to estimate parameters and test hypotheses for the study the evolutionary
process using trees reconstructed with programs such as PAUP*, PHYLIP, MOLPHY,
PhyML, or RaxML.
MAPMAKER/EXP is a linkage analysis package designed to help construct primary
linkage maps of markers segregating in experimental crosses. MAPMAKER/EXP
performs full multipoint linkage analysis (simultaneous estimation of all
recombination fractions from the primary data) for dominant, recessive, and co-
dominant (e.g. RFLP-like) markers. MAPMAKER/EXP is an experimental-cross-only
successor to the original MAPMAKER program.
MAPMAKER/QTL is a companion program to MAPMAKER/EXP which allows one to map
genes controlling polygenic quantitative traits in F2 intercrosses and BC1
backcrosses relative to a genetic linkage map. More information on MAPMAKER/QTL
can be found in the technical report (included with MAPMAKER/QTL).