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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.

Jalview is a multiple alignment editor written in Java. It is used widely in a variety of web pages (e.g. the EBI Clustalw server and the Pfam protein domain database) and is also available as a general purpose alignment editor. o Reads and writes alignments in a variety of formats o Gaps can be inserted/deleted using the mouse. o Group editing (insertion deletion of gaps in groups of sequences). o Removal of gapped columns. o Align sequences using Web Services (Clustal, Muscle...) o Amino acid conservation analysis similar to that of AMAS. o Alignment sorting options (by name, tree order, percent identity, group). o UPGMA and NJ trees calculated and drawn based on percent identity distances. o Sequence clustering using principal component analysis. o Removal of redundant sequences. o Smith Waterman pairwise alignment of selected sequences. o Web based secondary structure prediction programs (JNet). o User predefined or custom colour schemes to colour alignments or groups. o Sequence feature retrieval and display on the alignment. o Print your alignment with colours and annotations. o Output alignments as HTML pages, images (PNG) or postscript (EPS). If you use Jalview in your work, please quote this publication. Clamp, M., et al. (2004), The Jalview Java Alignment Editor. Bioinformatics, 12, 426-7

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.

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). Citation: Velvet: algorithms for de novo short read assembly using de Bruijn graphs. D.R. Zerbino and E. Birney. Genome Research 18: 821-829 (2008)

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/

TreeView X is program to display phylogenetic trees on Unix-like platforms. It can read and display NEXUS and Newick format tree files (such as those output by PAUP*, ClustalX, TREE-PUZZLE, and other programs). It has a subset of the functionality of the version of TreeView available for the Mac Classic and Windows (it is roughly equivalent to version 0.95 of TreeView).

dxf2fig parses Autocad DXF input, then calls external routines to do either plotting or a fig conversion for xfig. The conversion is fairly complete. Layers (depths in xfig), blocks (compounds in xfig), colors, and linetypes are roughly preserved in the output file.