Libsequence A C++ library designed to aid writing applications for genomics and evolutionary genetics. Ms The gold standard in coalescent simulations for population genetics. SimuPOP Highly modular and customizeable forward population genetic simulation software. Squint- A sequence editor with automated alignment, translation, etc. Uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.
Structure Population genetic analysis of admixture. LDhat LDhat is a package written in the C language for the analysis of recombination rates from population genetic data. It is supposed to specialize in bioinformatics functions Still in development, blocks have to be written by the user. SciCraft - Add-on to Octave, clones Simulink. There is a graphical menu for bioinformatics programs, as well as easy access to the Bio-Linux bioinformatics documentation system and sample data useful for testing programs. Bio-Linux provides more than 500 bioinformatics programs on an Ubuntu Linux base. Integrates tool for HMM profile search, multiple sequence alignment, PCR primers design, protein secondary structure prediction and others.īio-Linux 5.0 - a fully featured, powerful, configurable and easy to maintain bioinformatics workstation. UGENE - an integrated bioinformatics suite with handy visual interface. Tree-puzzle - TREE-PUZZLE is a computer program to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood.ĭIALIGN2 - a command line tool to perform multiple alignment of protein or DNA sequences. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). Tree View X - Tree View X is an open source program to display phylogenetic trees on Linux, Unix, Mac OS X, and Windows platforms. Phylip - A Package of programs for inferring phylogenies. Seaview - A sequence editor with multiple alignment (via ClustalW) and other capabilities In the authors tests, MUSCLE achieved the highest scores of all tested programs on several alignment accuracy benchmarks, and is also one of the fastest programs out there MUSCLE stands for multiple sequence comparison by log-expectation. Muscle - A program for multiple alignment of protein sequences. ClustalX is a GUI front end for ClustalW.Įmboss - a suite of bioinformatics tools. Ubuntu Linux includes many packages useful for biologists.īioPerl - a collection of Perl modules that are useful for programmers in bioinformatics/biologyĬlustalw - This program performs an alignment of multiple nucleotide or amino acid sequences.
The aim of this page is to become a useful resource for biologists and students using Ubuntu (or any other) Linux.
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