Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format
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Oct 15, 2010 - C++
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synteny
Here are 36 public repositories matching this topic...
Guided synteny alignment between duplicated genomes (within specified quota constraint)
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Sep 5, 2017 - Python
Bioinformatics pipeline for binding sites prediction
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Apr 16, 2018 - Jupyter Notebook
Genome assembly scaffolding using information from paired-end/mate-pair 8000 libraries, long reads, and synteny to closely related species.
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Dec 6, 2018 - Python
Trace intervals between genomes using a synteny map
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Mar 24, 2019 - C++
Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints
visualization bioinformatics pipeline genome mapping scaffold dna alignment circos synteny act bioinformatics-analysis chromosome contigs assemblies smalt misjoint rearrengment inter-chromosomes minimap2
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May 24, 2020 - C++
Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, dire…
visualization svg bioinformatics vcf depth snp comparative-genomics bam synteny transcriptomics genomes sv read-mapping long-reads genome-viewer crosslink genecluster structure-variation indel igv-like
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Jul 12, 2020 - HTML
R package for the reproducible detection of synteny blocks using genetic map data
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Feb 9, 2021 - R
AccuSyn: An Accurate Web-based Genome Synteny Browser
react javascript d3 bioinformatics genetics optimization data-visualization information-visualization circos simulated-annealing comparative-genomics synteny circos-graphs heuristic-search d3-visualization mcscanx
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Aug 27, 2024 - JavaScript
Set clinker to be run remotely from a server
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Aug 29, 2021 - PHP
CoGe (Comparative Genomics) Platform
python bioinformatics rna-seq genomics perl comparative-genomics coge synteny genomics-visualization
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Dec 21, 2021 - Perl
CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology
evolution duplication comparative-genomics transposition synteny copy-number-variation structural-variation convergent-evolution orthologs co-linearity
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Jun 9, 2022 - Python
Finding regions of similarity between plasmids
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Nov 2, 2022 - Nextflow
A visualization tool for viewing MCscanX Synteny Collinearity files (outdated please check description or readme)
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Dec 8, 2022 - JavaScript
A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes
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Feb 15, 2023 - Java
Custom scripts and workflows used in the genomics and population analysis of oat crown rust (Puccinia coronata f. sp. avenae) preprint (bioRxiv 2023.09.18.557855). All steps performed in Linux environment or R.
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Sep 21, 2023 - Python
Query sequence database by HMMs arranged in predefined synteny structure
python hmm bioinformatics genomics computational-biology metagenomics synteny hmmer prokaryotic-genomes synteny-block
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Nov 3, 2023 - Python
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