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pyScaf
By Bulbul 2898 days agogithub.com - pyScaf orders contigs from genome assemblies utilising several types of information: paired-end (PE) and/or mate-pair libraries (NGS-based mode) long reads (NGS-based mode) synteny to the genome of some related species (reference-based...MCscan
By Bulbul 2895 days agochibba.agtec.uga.edu - MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences...YAHA
By Jit 2866 days agowww.ncbi.nlm.nih.gov - YAHA, a fast and flexible hash-based aligner. YAHA is as fast and accurate as BWA-SW at finding the single best alignment per query and is dramatically faster and more sensitive than both SSAHA2 and MegaBLAST at finding all possible alignments....sockeye
By Jit 2838 days agowww.bcgsc.ca - This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects...Dynamic Programming Alignment
By Jitendra Narayan 4113 days agolecture 9, Chem. C100, Spring 2013, UCLACONCOCT: Clustering cONtigs with COverage and ComposiTion
By Jit 2821 days agogithub.com - A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. Warning! This software is to be considered under development. Functionality and the...Tetra-Nucleotide Analysis
By Jit 2762 days agochunlab.wordpress.com - A tetra-nucleotide is a fragment of DNA sequence with 4 bases (e.g. AGTC or TTGG). Pride et al. (2003) showed that the frequency of tetra-nucleotides in bacterial genomes contain useful, albeit weak, phylogenetic signals. Even though...HTSlib
By Jit 2812 days agohttp://www.htslib.org/ - Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: SamtoolsReading/writing/editing/indexing/viewing SAM/BAM/CRAM formatBCFtoolsReading/writing BCF2/VCF/gVCF files and...International Conference on Bioinformatics Models, Methods and Algorithms
By Rahul Agarwal 3704 days agowww.bioinformatics.biostec.org - The purpose of the International Conference on Bioinformatics Models, Methods and Algorithms is to bring together researchers and practitioners interested in the application of computational systems and information technologies to the field of...scikit-bio™ is an open-source, BSD-licensed, python package providing data structures, algorithms,...
By Jit 2460 days agohttp://scikit-bio.org/ - scikit-bio is currently in beta. We are very actively developing it, and backward-incompatible interface changes can and will arise. To avoid these types of changes being a surprise to our users, our public APIs are decorated to make it clear...
