Ports Search

This program is a much more convient version of the ttcp program. It uses inetd (or simulates its behaviour) to start off the remote side program which will send/receive data. Both sides measure the time and number of bytes transfered. The local side will print the measures. The format of the output can be specified on the commandline.

The octave-forge package is the result of The GNU Octave Repositry project, which is intended to be a central location for custom scripts, functions and extensions for GNU Octave. contains the source for all the functions plus build and install scripts. This is benchmark. The package contains code used to benchmark speed of Octave.

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.

ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen via viewing Cladograms or Phylograms.

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.

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.

PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters.

PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.

The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome.

SeaView is a multiple sequence alignment editor. You can align DNA/protein sequences from several organisms, and find out their relative postions in phylogenic tree. Once SeaView is installed, you can open the on-line help window through the 'Help' button to learn how to use SeaView. Example mase files can be found at: ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/