Software Tools
COAL is an acronym for Cluster Overview of Archaeal Life. The purpose of COAL is to visualize protein orthology and to relate orthology with additional information derived from their genomes. This information includes phylogeny, ecotype, metabolism, thermal preference and aerobicity. The protein orthology networks are also subclustered, when possible, using a bipartioning approach based on spectral clustering.
This site provides access to simulated datasets and aims to facilitate standardized benchmarking of tools for metagenomic analysis. To evaluate methods currently used to process metagenomic sequences, simulated datasets of varying complexity were constructed by combining sequencing reads randomly selected from 113 isolate genomes. These datasets were designed to model real metagenomes in terms of complexity and phylogenetic composition.
GenePRIMP (Gene PRediction IMprovement Pipeline) is a pipeline that consists of a series of computational units that identify erroneous gene calls and missed genes and correct a subset of the identified defective features. The input to GenePRIMP needs to be a file of gene calls in GenBank or EMBL format. As its output, GenePRIMP generates reports of identified gene prediction anomalies.
JGI publishes all its sequenced genomes on its Genome Portal. Here you can download sequence files, BLAST against a particular genome, and view annotations. Advanced tools, including genome, GO, KEGG, and KOG browsers, are available for eukaryotes. JGI's Genome Browser lets you browse through JGI-predicted genes, view sequences, and study detailed alignments with nucleotide and amino acid sequences from relevant sequence databases.
The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis and annotation of all publicly available genomes from three domains of life, in a uniquely integrated context. IMG/M provides tools for analyzing the functional capability of microbial communities based on their metagenome sequence, in the context of reference isolate genomes included from the IMG system. IMG/EDU provides training and teaching support for genome analysis applied to the annotation of microbial genomes. IMG/ER provides support to individual scientists or groups of scientists for functional annotation and curation of microbial genomes of interest, usually prior to their release to Genbank.
The Metazome project organizes the proteomes of metazoans into gene families defined at ancestral nodes on the metazoan evolutionary tree. Users can study the evolutionary history of a gene of interest from one of the included proteomes or place a gene from a different organism in the most appropriate gene family. Alternatively, you can BLAST search and browse the genomes of any of the included metazoans. You can easily move back and forth between organism-centric and gene family-centric views.
The Phytozome project organizes the proteomes of green plants into gene families defined at nodes on the green plant evolutionary tree. You can study the evolutionary history of a gene of interest from one of the included proteomes or place a gene from a different plant in the most appropriate gene family. Alternatively, you can BLAST search and browse the genomes of any of the included green plants. Phytozome makes it easy to move back and forth between organism-centric and gene family-centric views.
VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species.
