• AVID

  • Referenced in 11 articles [sw17110]
  • large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative...
  • CVTree3

  • Referenced in 6 articles [sw22015]
  • CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy ... genome data. With the number of sequenced genomes reaching tens of thousands, both tree inference ... latest Release 3.0 of the alignment-free and whole-genome-based web server CVTree3...
  • Cgaln

  • Referenced in 2 articles [sw22989]
  • Cgaln: fast and space-efficient whole-genome alignment. BACKGROUND: Whole-genome sequence alignment ... whole-genome sequences within practical amounts of time and space. However, most existing genomic alignment ... with those of other programs on whole genomic sequences of several bacteria and of some ... hours to finish an alignment between the whole genomes of human and mouse...
  • eHive

  • Referenced in 2 articles [sw27408]
  • implementation of three pipelines: (1) pairwise whole genome alignments, (2) multiple whole genome alignments...
  • Mugsy

  • Referenced in 4 articles [sw16994]
  • Mugsy: fast multiple alignment of closely related whole genomes. Motivation: The relative ease ... tools that can quickly compare multiple whole-genome sequences, millions of base pairs in length ... present a new multiple alignment tool for whole genomes named Mugsy. Mugsy is computationally efficient...
  • MAVID

  • Referenced in 1 article [sw23117]
  • Aligning multiple whole genomes with Mercator and MAVID. The availability of an increasing number ... whole genome sequences presents us with the need for tools to quickly put them into ... accomplish this task. Given multiple whole genomes as input, Mercator is first used to construct ... researcher through the steps required for whole-genome alignment with Mercator and MAVID...
  • HAPLOWSER

  • Referenced in 1 article [sw38315]
  • that depicts a global picture of whole-genome alignments among haplotypes of different organisms ... introduce a whole-genome HAPLotype brOWSER (HAPLOWSER), providing evolutionary perspectives from multiple aligned haplotypes...
  • BFAST

  • Referenced in 4 articles [sw20962]
  • BFAST: an alignment tool for large scale genome resequencing. Background: The new generation of massively ... whole human genome resequencing, result in the need for rapid and accurate alignment of billions ... reference genome. Speed is obviously of great importance, but equally important is maintaining alignment accuracy ... flexible, efficient whole genome indexes to rapidly map reads to candidate alignment locations, with arbitrary...
  • ExaML

  • Referenced in 1 article [sw29594]
  • inferring phylogenies on whole-transcriptome and whole-genome alignments using supercomputers. Results: We introduce several...
  • snoSeeker

  • Referenced in 1 article [sw15009]
  • have systematically scanned four human-mammal whole-genome alignment (WGA) sequences and identified 54 novel...
  • BSmooth

  • Referenced in 11 articles [sw23483]
  • which can now be measured using whole-genome bisulfite sequencing. However, cost, complexity ... widely applied. Here we present BSmooth, an alignment, quality control and analysis pipeline that provides...
  • HISAT

  • Referenced in 5 articles [sw28860]
  • HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads ... global FM index that represents a whole genome, HISAT uses a large set of small ... that collectively cover the whole genome (each index represents a genomic region ... human genome). These small indexes (called local indexes) combined with several alignment strategies enable effective...
  • CYNTENATOR

  • Referenced in 1 article [sw29670]
  • CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes. Whole genome gene order evolution ... genomes. It became apparent that other factors exist that constrain gene order in some genomic ... evolutionary time periods. Outside of these regions, genomes diverge more rapidly in terms of gene ... have developed CYNTENATOR, a progressive gene order alignment software, to identify genomic regions of conserved...
  • SNVMix

  • Referenced in 4 articles [sw29569]
  • Next-generation sequencing (NGS) has enabled whole genome and transcriptome single nucleotide variant (SNV) discovery ... millions of short sequence reads that, once aligned to a reference genome sequence...
  • BaCelLo

  • Referenced in 9 articles [sw17174]
  • subcellular location of proteins in large scale genomic projects. Results. BaCelLo is a predictor ... evolutionary information contained in alignment profiles. It analyzes the whole sequence composition and the compositions...
  • Crossbow

  • Referenced in 2 articles [sw34367]
  • whole genome resequencing analysis. It combines Bowtie, an ultrafast and memory efficient short read aligner...
  • PCAP

  • Referenced in 3 articles [sw17185]
  • genome assembly program. We describe a whole-genome assembly program named PCAP for processing tens ... contig is based on an alignment of reads in the contig, in which both base ... program was tested on a mouse whole-genome data set of 30 million reads...
  • BSMAP

  • Referenced in 5 articles [sw23515]
  • BSMAP: whole genome bisulfite sequence MAPping program. BACKGROUND: Bisulfite sequencing is a powerful technique ... genome. However, mapping high-throughput bisulfite reads to the reference genome remains a great challenge ... bisulfite sequence, asymmetric cytosine to thymine alignments, and multiple CpG heterogeneous methylation. RESULTS: We developed ... address the above issues. BSMAP combines genome hashing and bitwise masking to achieve fast...
  • HMM-Fisher

  • Referenced in 4 articles [sw28769]
  • sites (DMCs) and regions (DMRs) from whole genome and targeted bisulfite sequencing (BS) data. This ... their status and distance. This program takes aligned BS data in multiple samples and outputs...
  • PICS

  • Referenced in 3 articles [sw37329]
  • short-read sequencing. While it can profile genome-wide in vivo transcription factor-DNA association ... identifying regions bound by transcription factors from aligned reads. PICS identifies binding event locations ... mixture model. It uses precalculated, whole-genome read mappability profiles and a truncated (t)-distribution...