BamView: a free interactive display of read alignments in BAM data files
To run the application on UNIX from the downloaded jar file run the UNIX: java -mx512m -jar BamView.jar and extra c...index file should have the same name as the BAM file but with a '.bai' suffix. Multi...2048 days ago
ANItools web: a web tool for fast genome comparison within multiple bacterial strains
ANItools is a software package written by PERL scripts that can be run in a Linux/Unix system. If you want to compare bacterial genomes and calculate their average nuc...2043 days ago
BLAST options, setting and defaults
BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al....d different results from BLAST, and may be useful for motif searching, is FASTA. To search nonplant datasets,...2017 days ago
KEGG Mapper – Reconstruct Pathway
Reconstruct Pathway is a KEGG PATHWAY mapping tool that assists genome and metagenome annotations. The input data is a single gene list (for a single organism) or multiple gene lists (for multi...2015 days ago
EGAD: Ultra-fast functional analysis of gene networks
With the EGAD (Extending ‘Guilt-by-Association’ by Degree) package, we present a series of highly efficie...n analytic determination of the optimal prior to guess candidates genes across multi...2013 days ago
ARCS: scaffolding genome drafts with linked reads
ARCS requires two input files: Draft assembly fasta file Interleaved linked reads file (Barcode sequence expected in the BX tag of the read header or in the form "@readname_barcode" ; Run Long Ranger basic on raw chromium reads to produce this interleaved file)2010 days ago
FGENESH - Program for predicting multiple genes in genomic DNA sequences
FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencin...2007 days ago
GenomeView: genome browser and annotation editor
GenomeView is a genome browser and annotation editor that displays reference sequence, annotation, multi...1994 days ago
MCAT: Motif Combining and Association Tool
This is a pipeline for finding motifs in fasta files.It can be run from the command line as follows:...seq negative_seq positional arguments:positive_seq the fasta file for the positive sequencesnegative_seq the fasta file for the negative sequenc...1983 days ago
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