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PhD program in Computer Science at University of Essex
As part of the PhD program in Computer Science at University of Essex, I am looking for a PhD student in computational and synthetic biology. The ideal candidate is interested in designing new biological design automation methods for genome scale...
BioDownloader
By Surabhi Chaudhary 3297 days agodunbrack.fccc.edu - BioDownloader is a program for downloading and/or updating files from ftp/http servers. The program has unique features that are specifically designed to deal with bioinformatics data files and servers: optimized to work with vast amount of data...DAGchainer: Computing Chains of Syntenic Genes in Complete Genomes
By Abhimanyu Singh 3305 days agodagchainer.sourceforge.net - The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts...ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
By Jit 3298 days agogithub.com - ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, they report findings regarding errors in sequencing. The method can...CGView - Circular Genome Viewer
By Rahul Nayak 2817 days agowishart.biology.ualberta.ca - CGView is a Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web. Feature...PBSuite: Software for Long-Read Sequencing Data from PacBio
By Jit 3295 days agosourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...GeneMates: an R package for Detecting Horizontal Gene Co-transfer between Bacteria Using Gene-gene...
By Rahul Nayak 2191 days agogithub.com - GeneMates is an R package implementing a network approach to identify horizontal gene co-transfer (HGcoT) between bacteria using whole-genome sequencing (WGS) data. It is particularly useful for investigating intra-species HGcoT, where...MyCC: Accurate binning of metagenomic contigs via automated clustering sequences using information...
By Jit 3291 days agosourceforge.net - MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. More...
